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...@@ -20,6 +20,7 @@ _Team-Computer software (2016)_ ...@@ -20,6 +20,7 @@ _Team-Computer software (2016)_
**Source code**: [https://github.com/mamba-org/mamba](https://github.com/mamba-org/mamba) (mamba) **Source code**: [https://github.com/mamba-org/mamba](https://github.com/mamba-org/mamba) (mamba)
**Documentation**: [https://mamba.readthedocs.io/en/latest/index.html](https://mamba.readthedocs.io/en/latest/index.html) (mamba) **Documentation**: [https://mamba.readthedocs.io/en/latest/index.html](https://mamba.readthedocs.io/en/latest/index.html) (mamba)
## Havoc
**HAVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences** **HAVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences**
Phuoc Thien Truong Nguyen, Ilya Plyusnin, Tarja Sironen, Olli Vapalahti, Ravi Kant & Teemu Smura Phuoc Thien Truong Nguyen, Ilya Plyusnin, Tarja Sironen, Olli Vapalahti, Ravi Kant & Teemu Smura
_BMC Bioinformatics volume 22, Article number: 373 (2021)_ _BMC Bioinformatics volume 22, Article number: 373 (2021)_
...@@ -28,6 +29,7 @@ _BMC Bioinformatics volume 22, Article number: 373 (2021)_ ...@@ -28,6 +29,7 @@ _BMC Bioinformatics volume 22, Article number: 373 (2021)_
**Source code**: [https://bitbucket.org/auto_cov_pipeline/havoc](https://bitbucket.org/auto_cov_pipeline/havoc) **Source code**: [https://bitbucket.org/auto_cov_pipeline/havoc](https://bitbucket.org/auto_cov_pipeline/havoc)
**Documentation**: [https://www2.helsinki.fi/en/projects/havoc](https://www2.helsinki.fi/en/projects/havoc) **Documentation**: [https://www2.helsinki.fi/en/projects/havoc](https://www2.helsinki.fi/en/projects/havoc)
## Nextclade
**Nextclade: clade assignment, mutation calling and quality control for viral genomes** **Nextclade: clade assignment, mutation calling and quality control for viral genomes**
Ivan Aksamentov, Cornelius Roemer, Emma B. Hodcroft and Richard A. Neher Ivan Aksamentov, Cornelius Roemer, Emma B. Hodcroft and Richard A. Neher
_The Journal of Open Source Software_ _The Journal of Open Source Software_
...@@ -36,6 +38,7 @@ _The Journal of Open Source Software_ ...@@ -36,6 +38,7 @@ _The Journal of Open Source Software_
**Source code**: [https://github.com/nextstrain/nextclade](https://github.com/nextstrain/nextclade) **Source code**: [https://github.com/nextstrain/nextclade](https://github.com/nextstrain/nextclade)
**Documentation**: [https://clades.nextstrain.org](https://clades.nextstrain.org) **Documentation**: [https://clades.nextstrain.org](https://clades.nextstrain.org)
## Pangolin
**Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool** **Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool**
Áine O’Toole, Emily Scher, Anthony Underwood, Ben Jackson, Verity Hill, John T McCrone, Rachel Colquhoun, Chris Ruis, Khalil Abu-Dahab, Ben Taylor, Corin Yeats, Louis du Plessis, Daniel Maloney, Nathan Medd, Stephen W Attwood, David M Aanensen, Edward C Holmes, Oliver G Pybus and Andrew Rambaut Áine O’Toole, Emily Scher, Anthony Underwood, Ben Jackson, Verity Hill, John T McCrone, Rachel Colquhoun, Chris Ruis, Khalil Abu-Dahab, Ben Taylor, Corin Yeats, Louis du Plessis, Daniel Maloney, Nathan Medd, Stephen W Attwood, David M Aanensen, Edward C Holmes, Oliver G Pybus and Andrew Rambaut
_Virus Evolution, Volume 7, Issue 2 (2021)_ _Virus Evolution, Volume 7, Issue 2 (2021)_
...@@ -45,6 +48,7 @@ _Virus Evolution, Volume 7, Issue 2 (2021)_ ...@@ -45,6 +48,7 @@ _Virus Evolution, Volume 7, Issue 2 (2021)_
**Source code**: [https://github.com/cov-lineages/scorpio](https://github.com/cov-lineages/scorpio) _(scorpio)_ **Source code**: [https://github.com/cov-lineages/scorpio](https://github.com/cov-lineages/scorpio) _(scorpio)_
**Documentation**: [https://cov-lineages.org/index.html](https://cov-lineages.org/index.html) **Documentation**: [https://cov-lineages.org/index.html](https://cov-lineages.org/index.html)
## Tabix
**Tabix: fast retrieval of sequence features from generic TAB-delimited files** **Tabix: fast retrieval of sequence features from generic TAB-delimited files**
Heng Li Heng Li
_Bioinformatics, Volume 27, Issue 5 (2011)_ _Bioinformatics, Volume 27, Issue 5 (2011)_
...@@ -53,6 +57,7 @@ _Bioinformatics, Volume 27, Issue 5 (2011)_ ...@@ -53,6 +57,7 @@ _Bioinformatics, Volume 27, Issue 5 (2011)_
**Source code**: [https://github.com/samtools/samtools](https://github.com/samtools/samtools) **Source code**: [https://github.com/samtools/samtools](https://github.com/samtools/samtools)
**Documentation**: [http://samtools.sourceforge.net](http://samtools.sourceforge.net) **Documentation**: [http://samtools.sourceforge.net](http://samtools.sourceforge.net)
## LoFreq
**LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets** **LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets**
Andreas Wilm, Pauline Poh Kim Aw, Denis Bertrand, Grace Hui Ting Yeo, Swee Hoe Ong, Chang Hua Wong, Chiea Chuen Khor, Rosemary Petric, Martin Lloyd Hibberd and Niranjan Nagarajan Andreas Wilm, Pauline Poh Kim Aw, Denis Bertrand, Grace Hui Ting Yeo, Swee Hoe Ong, Chang Hua Wong, Chiea Chuen Khor, Rosemary Petric, Martin Lloyd Hibberd and Niranjan Nagarajan
_Nucleic Acids Research, Volume 40, Issue 22 (2012)_ _Nucleic Acids Research, Volume 40, Issue 22 (2012)_
...@@ -62,6 +67,7 @@ _Nucleic Acids Research, Volume 40, Issue 22 (2012)_ ...@@ -62,6 +67,7 @@ _Nucleic Acids Research, Volume 40, Issue 22 (2012)_
**Source code**: [https://github.com/andreas-wilm/lofreq3](https://github.com/andreas-wilm/lofreq3) _(see also v3 in Nim)_ **Source code**: [https://github.com/andreas-wilm/lofreq3](https://github.com/andreas-wilm/lofreq3) _(see also v3 in Nim)_
**Documentation**: [https://csb5.github.io/lofreq](https://csb5.github.io/lofreq) **Documentation**: [https://csb5.github.io/lofreq](https://csb5.github.io/lofreq)
## NF-Core
**The nf-core framework for community-curated bioinformatics pipelines** **The nf-core framework for community-curated bioinformatics pipelines**
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen
_Nat Biotechnol. 2020 Feb 13_ _Nat Biotechnol. 2020 Feb 13_
...@@ -70,6 +76,8 @@ _Nat Biotechnol. 2020 Feb 13_ ...@@ -70,6 +76,8 @@ _Nat Biotechnol. 2020 Feb 13_
**Source code**: [https://github.com/nf-core/viralrecon](https://github.com/nf-core/viralrecon) **Source code**: [https://github.com/nf-core/viralrecon](https://github.com/nf-core/viralrecon)
**Documentation**: [https://nf-co.re/viralrecon/usage](https://nf-co.re/viralrecon/usage) **Documentation**: [https://nf-co.re/viralrecon/usage](https://nf-co.re/viralrecon/usage)
## iVar
**iVar, an Interpretation-Oriented Tool to Manage the Update and Revision of Variant Annotation and Classification** **iVar, an Interpretation-Oriented Tool to Manage the Update and Revision of Variant Annotation and Classification**
Sara Castellano, Federica Cestari, Giovanni Faglioni, Elena Tenedini, Marco Marino, Lucia Artuso, Rossella Manfredini, Mario Luppi, Tommaso Trenti and Enrico Tagliafico Sara Castellano, Federica Cestari, Giovanni Faglioni, Elena Tenedini, Marco Marino, Lucia Artuso, Rossella Manfredini, Mario Luppi, Tommaso Trenti and Enrico Tagliafico
_Genes, Volume 12(3), Issue 384 (2021)_ _Genes, Volume 12(3), Issue 384 (2021)_
...@@ -78,6 +86,7 @@ _Genes, Volume 12(3), Issue 384 (2021)_ ...@@ -78,6 +86,7 @@ _Genes, Volume 12(3), Issue 384 (2021)_
**Source code**: [https://github.com/andersen-lab/ivar](https://github.com/andersen-lab/ivar) **Source code**: [https://github.com/andersen-lab/ivar](https://github.com/andersen-lab/ivar)
**Documentation**: [https://andersen-lab.github.io/ivar/html/manualpage.html](https://andersen-lab.github.io/ivar/html/manualpage.html) **Documentation**: [https://andersen-lab.github.io/ivar/html/manualpage.html](https://andersen-lab.github.io/ivar/html/manualpage.html)
## AWK
**The AWK Programming Language** **The AWK Programming Language**
Al Aho, Brian Kernighan and Peter Weinberger Al Aho, Brian Kernighan and Peter Weinberger
_Addison-Wesley (1988)_ _Addison-Wesley (1988)_
...@@ -86,6 +95,8 @@ _Addison-Wesley (1988)_ ...@@ -86,6 +95,8 @@ _Addison-Wesley (1988)_
**Source code**: [https://github.com/onetrueawk/awk](https://github.com/onetrueawk/awk) **Source code**: [https://github.com/onetrueawk/awk](https://github.com/onetrueawk/awk)
**Documentation**: [https://www.gnu.org/software/gawk/manual/gawk.html](https://www.gnu.org/software/gawk/manual/gawk.html) **Documentation**: [https://www.gnu.org/software/gawk/manual/gawk.html](https://www.gnu.org/software/gawk/manual/gawk.html)
## BED-tools
**BEDTools: a flexible suite of utilities for comparing genomic features** **BEDTools: a flexible suite of utilities for comparing genomic features**
Aaron R. Quinlan and Ira M. Hall Aaron R. Quinlan and Ira M. Hall
_Bioinformatics, Volume 26, Issue 6 (2010)_ _Bioinformatics, Volume 26, Issue 6 (2010)_
...@@ -94,6 +105,7 @@ _Bioinformatics, Volume 26, Issue 6 (2010)_ ...@@ -94,6 +105,7 @@ _Bioinformatics, Volume 26, Issue 6 (2010)_
**Source code**: [https://github.com/arq5x/bedtools2](https://github.com/arq5x/bedtools2) **Source code**: [https://github.com/arq5x/bedtools2](https://github.com/arq5x/bedtools2)
**Documentation**: [https://bedtools.readthedocs.io/en/latest/](https://bedtools.readthedocs.io/en/latest/) **Documentation**: [https://bedtools.readthedocs.io/en/latest/](https://bedtools.readthedocs.io/en/latest/)
## ARTIC
**ARTIC Network** **ARTIC Network**
Authors Authors
Journal (year) Journal (year)
...@@ -102,6 +114,7 @@ Journal (year) ...@@ -102,6 +114,7 @@ Journal (year)
**Source code**: [https://github.com/artic-network/primer-schemes](https://github.com/artic-network/primer-schemes) **Source code**: [https://github.com/artic-network/primer-schemes](https://github.com/artic-network/primer-schemes)
**Documentation**: **Documentation**:
## SAM-tools / BCF-tools
**Twelve years of SAMtools and BCFtools** **Twelve years of SAMtools and BCFtools**
Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin O Pollard, Andrew Whitwham, Thomas Keane, Shane A McCarthy, Robert M Davies and Heng Li Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin O Pollard, Andrew Whitwham, Thomas Keane, Shane A McCarthy, Robert M Davies and Heng Li
_GigaScience, Volume 10, Issue 2 (2021)_ _GigaScience, Volume 10, Issue 2 (2021)_
...@@ -110,6 +123,7 @@ _GigaScience, Volume 10, Issue 2 (2021)_ ...@@ -110,6 +123,7 @@ _GigaScience, Volume 10, Issue 2 (2021)_
**Source code**: [https://github.com/samtools/samtools](https://github.com/samtools/samtools) **Source code**: [https://github.com/samtools/samtools](https://github.com/samtools/samtools)
**Documentation**: [http://samtools.sourceforge.net](http://samtools.sourceforge.net) **Documentation**: [http://samtools.sourceforge.net](http://samtools.sourceforge.net)
## Minimap2
**Minimap2: pairwise alignment for nucleotide sequences** **Minimap2: pairwise alignment for nucleotide sequences**
Heng Li Heng Li
_Bioinformatics, Volume 34, Issue 18 (2018)_ _Bioinformatics, Volume 34, Issue 18 (2018)_
...@@ -118,6 +132,7 @@ _Bioinformatics, Volume 34, Issue 18 (2018)_ ...@@ -118,6 +132,7 @@ _Bioinformatics, Volume 34, Issue 18 (2018)_
**Source code**: [https://github.com/lh3/minimap2](https://github.com/lh3/minimap2) **Source code**: [https://github.com/lh3/minimap2](https://github.com/lh3/minimap2)
**Documentation**: [https://lh3.github.io/minimap2/minimap2.html](https://lh3.github.io/minimap2/minimap2.html) **Documentation**: [https://lh3.github.io/minimap2/minimap2.html](https://lh3.github.io/minimap2/minimap2.html)
## BWA
**Fast and accurate short read alignment with Burrows-Wheeler Transform** **Fast and accurate short read alignment with Burrows-Wheeler Transform**
Heng Li and Richard Durbin Heng Li and Richard Durbin
_Bioinformatics, Volume 25, Aricle 1754-60 (2009)_ _Bioinformatics, Volume 25, Aricle 1754-60 (2009)_
...@@ -126,6 +141,7 @@ _Bioinformatics, Volume 25, Aricle 1754-60 (2009)_ ...@@ -126,6 +141,7 @@ _Bioinformatics, Volume 25, Aricle 1754-60 (2009)_
**Source code**: [https://github.com/lh3/bwa](https://github.com/lh3/bwa) **Source code**: [https://github.com/lh3/bwa](https://github.com/lh3/bwa)
**Documentation**: [http://bio-bwa.sourceforge.net](http://bio-bwa.sourceforge.net) **Documentation**: [http://bio-bwa.sourceforge.net](http://bio-bwa.sourceforge.net)
## Sickle-trim
**Sickle: A sliding-window, adaptive, quality-based trimming tool for FastQ files** **Sickle: A sliding-window, adaptive, quality-based trimming tool for FastQ files**
Joshi NA and Fass JN Joshi NA and Fass JN
_(2011) _(2011)
...@@ -134,6 +150,7 @@ _(2011) ...@@ -134,6 +150,7 @@ _(2011)
**Source code**: [https://github.com/najoshi/sickle](https://github.com/najoshi/sickle) **Source code**: [https://github.com/najoshi/sickle](https://github.com/najoshi/sickle)
**Documentation**: []() **Documentation**: []()
## Cutadapt
**Cutadapt Removes Adapter Sequences From High-Throughput Sequencing Reads** **Cutadapt Removes Adapter Sequences From High-Throughput Sequencing Reads**
Marcel Martin Marcel Martin
_EMBnet Journal, Volume 17, Article 1 (2011) _EMBnet Journal, Volume 17, Article 1 (2011)
...@@ -142,6 +159,7 @@ _EMBnet Journal, Volume 17, Article 1 (2011) ...@@ -142,6 +159,7 @@ _EMBnet Journal, Volume 17, Article 1 (2011)
**Source code**: [https://github.com/marcelm/cutadapt](https://github.com/marcelm/cutadapt) **Source code**: [https://github.com/marcelm/cutadapt](https://github.com/marcelm/cutadapt)
**Documentation**: [https://cutadapt.readthedocs.io/en/stable/](https://cutadapt.readthedocs.io/en/stable) **Documentation**: [https://cutadapt.readthedocs.io/en/stable/](https://cutadapt.readthedocs.io/en/stable)
## MultiQC
**MultiQC: summarize analysis results for multiple tools and samples in a single report** **MultiQC: summarize analysis results for multiple tools and samples in a single report**
Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
_Bioinformatics, Volume 32, Issue 19 (2016)_ _Bioinformatics, Volume 32, Issue 19 (2016)_
...@@ -150,6 +168,7 @@ _Bioinformatics, Volume 32, Issue 19 (2016)_ ...@@ -150,6 +168,7 @@ _Bioinformatics, Volume 32, Issue 19 (2016)_
**Source code**: [https://github.com/ewels/MultiQC](https://github.com/ewels/MultiQC) **Source code**: [https://github.com/ewels/MultiQC](https://github.com/ewels/MultiQC)
**Documentation**: [https://multiqc.info](https://multiqc.info) **Documentation**: [https://multiqc.info](https://multiqc.info)
## FastQ-Screen
**FastQ Screen: A tool for multi-genome mapping and quality control** **FastQ Screen: A tool for multi-genome mapping and quality control**
Wingett SW and Andrews S Wingett SW and Andrews S
_F1000Research (2018)_ _F1000Research (2018)_
...@@ -158,6 +177,7 @@ _F1000Research (2018)_ ...@@ -158,6 +177,7 @@ _F1000Research (2018)_
**Source code**: [https://github.com/StevenWingett/FastQ-Screen](https://github.com/StevenWingett/FastQ-Screen) **Source code**: [https://github.com/StevenWingett/FastQ-Screen](https://github.com/StevenWingett/FastQ-Screen)
**Documentation**: [https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen) **Documentation**: [https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen)
## FastQC
**FastQC: A quality control tool for high throughput sequence data** **FastQC: A quality control tool for high throughput sequence data**
Simon Andrews Simon Andrews
_Online (2010)_ _Online (2010)_
...@@ -166,6 +186,7 @@ _Online (2010)_ ...@@ -166,6 +186,7 @@ _Online (2010)_
**Source code**: [https://github.com/s-andrews/FastQC](https://github.com/s-andrews/FastQC) **Source code**: [https://github.com/s-andrews/FastQC](https://github.com/s-andrews/FastQC)
**Documentation**: [https://www.bioinformatics.babraham.ac.uk/projects/fastqc](https://www.bioinformatics.babraham.ac.uk/projects/fastqc) **Documentation**: [https://www.bioinformatics.babraham.ac.uk/projects/fastqc](https://www.bioinformatics.babraham.ac.uk/projects/fastqc)
## Seqtk
**Seqtk: A fast and lightweight tool for processing sequences in the FASTA or FASTQ format** **Seqtk: A fast and lightweight tool for processing sequences in the FASTA or FASTQ format**
Heng Li Heng Li
_Online (2014)_ _Online (2014)_
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# References
## Snakemake
**Sustainable data analysis with Snakemake** **Sustainable data analysis with Snakemake**
Felix Mölder, Kim Philipp Jablonski, Brice Letcher, Michael B. Hall, Christopher H. Tomkins-Tinch, Vanessa Sochat, Jan Forster, Soohyun Lee, Sven O. Twardziok, Alexander Kanitz, Andreas Wilm, Manuel Holtgrewe, Sven Rahmann, Sven Nahnsen, Johannes Köster Felix Mölder, Kim Philipp Jablonski, Brice Letcher, Michael B. Hall, Christopher H. Tomkins-Tinch, Vanessa Sochat, Jan Forster, Soohyun Lee, Sven O. Twardziok, Alexander Kanitz, Andreas Wilm, Manuel Holtgrewe, Sven Rahmann, Sven Nahnsen, Johannes Köster
_F1000Research (2021)_ _F1000Research (2021)_
...@@ -6,6 +9,8 @@ _F1000Research (2021)_ ...@@ -6,6 +9,8 @@ _F1000Research (2021)_
**Source code**: [https://github.com/snakemake/snakemake](https://github.com/snakemake/snakemake) **Source code**: [https://github.com/snakemake/snakemake](https://github.com/snakemake/snakemake)
**Documentation**: [https://snakemake.readthedocs.io/en/stable/index.html](https://snakemake.readthedocs.io/en/stable/index.html) **Documentation**: [https://snakemake.readthedocs.io/en/stable/index.html](https://snakemake.readthedocs.io/en/stable/index.html)
## Anaconda
**Anaconda Software Distribution** **Anaconda Software Distribution**
_Team-Computer software (2016)_ _Team-Computer software (2016)_
**DOI**: []() **DOI**: []()
...@@ -15,6 +20,7 @@ _Team-Computer software (2016)_ ...@@ -15,6 +20,7 @@ _Team-Computer software (2016)_
**Source code**: [https://github.com/mamba-org/mamba](https://github.com/mamba-org/mamba) (mamba) **Source code**: [https://github.com/mamba-org/mamba](https://github.com/mamba-org/mamba) (mamba)
**Documentation**: [https://mamba.readthedocs.io/en/latest/index.html](https://mamba.readthedocs.io/en/latest/index.html) (mamba) **Documentation**: [https://mamba.readthedocs.io/en/latest/index.html](https://mamba.readthedocs.io/en/latest/index.html) (mamba)
## Havoc
**HAVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences** **HAVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences**
Phuoc Thien Truong Nguyen, Ilya Plyusnin, Tarja Sironen, Olli Vapalahti, Ravi Kant & Teemu Smura Phuoc Thien Truong Nguyen, Ilya Plyusnin, Tarja Sironen, Olli Vapalahti, Ravi Kant & Teemu Smura
_BMC Bioinformatics volume 22, Article number: 373 (2021)_ _BMC Bioinformatics volume 22, Article number: 373 (2021)_
...@@ -23,6 +29,7 @@ _BMC Bioinformatics volume 22, Article number: 373 (2021)_ ...@@ -23,6 +29,7 @@ _BMC Bioinformatics volume 22, Article number: 373 (2021)_
**Source code**: [https://bitbucket.org/auto_cov_pipeline/havoc](https://bitbucket.org/auto_cov_pipeline/havoc) **Source code**: [https://bitbucket.org/auto_cov_pipeline/havoc](https://bitbucket.org/auto_cov_pipeline/havoc)
**Documentation**: [https://www2.helsinki.fi/en/projects/havoc](https://www2.helsinki.fi/en/projects/havoc) **Documentation**: [https://www2.helsinki.fi/en/projects/havoc](https://www2.helsinki.fi/en/projects/havoc)
## Nextclade
**Nextclade: clade assignment, mutation calling and quality control for viral genomes** **Nextclade: clade assignment, mutation calling and quality control for viral genomes**
Ivan Aksamentov, Cornelius Roemer, Emma B. Hodcroft and Richard A. Neher Ivan Aksamentov, Cornelius Roemer, Emma B. Hodcroft and Richard A. Neher
_The Journal of Open Source Software_ _The Journal of Open Source Software_
...@@ -31,6 +38,7 @@ _The Journal of Open Source Software_ ...@@ -31,6 +38,7 @@ _The Journal of Open Source Software_
**Source code**: [https://github.com/nextstrain/nextclade](https://github.com/nextstrain/nextclade) **Source code**: [https://github.com/nextstrain/nextclade](https://github.com/nextstrain/nextclade)
**Documentation**: [https://clades.nextstrain.org](https://clades.nextstrain.org) **Documentation**: [https://clades.nextstrain.org](https://clades.nextstrain.org)
## Pangolin
**Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool** **Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool**
Áine O’Toole, Emily Scher, Anthony Underwood, Ben Jackson, Verity Hill, John T McCrone, Rachel Colquhoun, Chris Ruis, Khalil Abu-Dahab, Ben Taylor, Corin Yeats, Louis du Plessis, Daniel Maloney, Nathan Medd, Stephen W Attwood, David M Aanensen, Edward C Holmes, Oliver G Pybus and Andrew Rambaut Áine O’Toole, Emily Scher, Anthony Underwood, Ben Jackson, Verity Hill, John T McCrone, Rachel Colquhoun, Chris Ruis, Khalil Abu-Dahab, Ben Taylor, Corin Yeats, Louis du Plessis, Daniel Maloney, Nathan Medd, Stephen W Attwood, David M Aanensen, Edward C Holmes, Oliver G Pybus and Andrew Rambaut
_Virus Evolution, Volume 7, Issue 2 (2021)_ _Virus Evolution, Volume 7, Issue 2 (2021)_
...@@ -40,6 +48,7 @@ _Virus Evolution, Volume 7, Issue 2 (2021)_ ...@@ -40,6 +48,7 @@ _Virus Evolution, Volume 7, Issue 2 (2021)_
**Source code**: [https://github.com/cov-lineages/scorpio](https://github.com/cov-lineages/scorpio) _(scorpio)_ **Source code**: [https://github.com/cov-lineages/scorpio](https://github.com/cov-lineages/scorpio) _(scorpio)_
**Documentation**: [https://cov-lineages.org/index.html](https://cov-lineages.org/index.html) **Documentation**: [https://cov-lineages.org/index.html](https://cov-lineages.org/index.html)
## Tabix
**Tabix: fast retrieval of sequence features from generic TAB-delimited files** **Tabix: fast retrieval of sequence features from generic TAB-delimited files**
Heng Li Heng Li
_Bioinformatics, Volume 27, Issue 5 (2011)_ _Bioinformatics, Volume 27, Issue 5 (2011)_
...@@ -48,6 +57,7 @@ _Bioinformatics, Volume 27, Issue 5 (2011)_ ...@@ -48,6 +57,7 @@ _Bioinformatics, Volume 27, Issue 5 (2011)_
**Source code**: [https://github.com/samtools/samtools](https://github.com/samtools/samtools) **Source code**: [https://github.com/samtools/samtools](https://github.com/samtools/samtools)
**Documentation**: [http://samtools.sourceforge.net](http://samtools.sourceforge.net) **Documentation**: [http://samtools.sourceforge.net](http://samtools.sourceforge.net)
## LoFreq
**LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets** **LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets**
Andreas Wilm, Pauline Poh Kim Aw, Denis Bertrand, Grace Hui Ting Yeo, Swee Hoe Ong, Chang Hua Wong, Chiea Chuen Khor, Rosemary Petric, Martin Lloyd Hibberd and Niranjan Nagarajan Andreas Wilm, Pauline Poh Kim Aw, Denis Bertrand, Grace Hui Ting Yeo, Swee Hoe Ong, Chang Hua Wong, Chiea Chuen Khor, Rosemary Petric, Martin Lloyd Hibberd and Niranjan Nagarajan
_Nucleic Acids Research, Volume 40, Issue 22 (2012)_ _Nucleic Acids Research, Volume 40, Issue 22 (2012)_
...@@ -57,6 +67,7 @@ _Nucleic Acids Research, Volume 40, Issue 22 (2012)_ ...@@ -57,6 +67,7 @@ _Nucleic Acids Research, Volume 40, Issue 22 (2012)_
**Source code**: [https://github.com/andreas-wilm/lofreq3](https://github.com/andreas-wilm/lofreq3) _(see also v3 in Nim)_ **Source code**: [https://github.com/andreas-wilm/lofreq3](https://github.com/andreas-wilm/lofreq3) _(see also v3 in Nim)_
**Documentation**: [https://csb5.github.io/lofreq](https://csb5.github.io/lofreq) **Documentation**: [https://csb5.github.io/lofreq](https://csb5.github.io/lofreq)
## NF-Core
**The nf-core framework for community-curated bioinformatics pipelines** **The nf-core framework for community-curated bioinformatics pipelines**
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen
_Nat Biotechnol. 2020 Feb 13_ _Nat Biotechnol. 2020 Feb 13_
...@@ -65,6 +76,8 @@ _Nat Biotechnol. 2020 Feb 13_ ...@@ -65,6 +76,8 @@ _Nat Biotechnol. 2020 Feb 13_
**Source code**: [https://github.com/nf-core/viralrecon](https://github.com/nf-core/viralrecon) **Source code**: [https://github.com/nf-core/viralrecon](https://github.com/nf-core/viralrecon)
**Documentation**: [https://nf-co.re/viralrecon/usage](https://nf-co.re/viralrecon/usage) **Documentation**: [https://nf-co.re/viralrecon/usage](https://nf-co.re/viralrecon/usage)
## iVar
**iVar, an Interpretation-Oriented Tool to Manage the Update and Revision of Variant Annotation and Classification** **iVar, an Interpretation-Oriented Tool to Manage the Update and Revision of Variant Annotation and Classification**
Sara Castellano, Federica Cestari, Giovanni Faglioni, Elena Tenedini, Marco Marino, Lucia Artuso, Rossella Manfredini, Mario Luppi, Tommaso Trenti and Enrico Tagliafico Sara Castellano, Federica Cestari, Giovanni Faglioni, Elena Tenedini, Marco Marino, Lucia Artuso, Rossella Manfredini, Mario Luppi, Tommaso Trenti and Enrico Tagliafico
_Genes, Volume 12(3), Issue 384 (2021)_ _Genes, Volume 12(3), Issue 384 (2021)_
...@@ -73,6 +86,7 @@ _Genes, Volume 12(3), Issue 384 (2021)_ ...@@ -73,6 +86,7 @@ _Genes, Volume 12(3), Issue 384 (2021)_
**Source code**: [https://github.com/andersen-lab/ivar](https://github.com/andersen-lab/ivar) **Source code**: [https://github.com/andersen-lab/ivar](https://github.com/andersen-lab/ivar)
**Documentation**: [https://andersen-lab.github.io/ivar/html/manualpage.html](https://andersen-lab.github.io/ivar/html/manualpage.html) **Documentation**: [https://andersen-lab.github.io/ivar/html/manualpage.html](https://andersen-lab.github.io/ivar/html/manualpage.html)
## AWK
**The AWK Programming Language** **The AWK Programming Language**
Al Aho, Brian Kernighan and Peter Weinberger Al Aho, Brian Kernighan and Peter Weinberger
_Addison-Wesley (1988)_ _Addison-Wesley (1988)_
...@@ -81,6 +95,8 @@ _Addison-Wesley (1988)_ ...@@ -81,6 +95,8 @@ _Addison-Wesley (1988)_
**Source code**: [https://github.com/onetrueawk/awk](https://github.com/onetrueawk/awk) **Source code**: [https://github.com/onetrueawk/awk](https://github.com/onetrueawk/awk)
**Documentation**: [https://www.gnu.org/software/gawk/manual/gawk.html](https://www.gnu.org/software/gawk/manual/gawk.html) **Documentation**: [https://www.gnu.org/software/gawk/manual/gawk.html](https://www.gnu.org/software/gawk/manual/gawk.html)
## BED-tools
**BEDTools: a flexible suite of utilities for comparing genomic features** **BEDTools: a flexible suite of utilities for comparing genomic features**
Aaron R. Quinlan and Ira M. Hall Aaron R. Quinlan and Ira M. Hall
_Bioinformatics, Volume 26, Issue 6 (2010)_ _Bioinformatics, Volume 26, Issue 6 (2010)_
...@@ -89,6 +105,7 @@ _Bioinformatics, Volume 26, Issue 6 (2010)_ ...@@ -89,6 +105,7 @@ _Bioinformatics, Volume 26, Issue 6 (2010)_
**Source code**: [https://github.com/arq5x/bedtools2](https://github.com/arq5x/bedtools2) **Source code**: [https://github.com/arq5x/bedtools2](https://github.com/arq5x/bedtools2)
**Documentation**: [https://bedtools.readthedocs.io/en/latest/](https://bedtools.readthedocs.io/en/latest/) **Documentation**: [https://bedtools.readthedocs.io/en/latest/](https://bedtools.readthedocs.io/en/latest/)
## ARTIC
**ARTIC Network** **ARTIC Network**
Authors Authors
Journal (year) Journal (year)
...@@ -97,6 +114,7 @@ Journal (year) ...@@ -97,6 +114,7 @@ Journal (year)
**Source code**: [https://github.com/artic-network/primer-schemes](https://github.com/artic-network/primer-schemes) **Source code**: [https://github.com/artic-network/primer-schemes](https://github.com/artic-network/primer-schemes)
**Documentation**: **Documentation**:
## SAM-tools / BCF-tools
**Twelve years of SAMtools and BCFtools** **Twelve years of SAMtools and BCFtools**
Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin O Pollard, Andrew Whitwham, Thomas Keane, Shane A McCarthy, Robert M Davies and Heng Li Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin O Pollard, Andrew Whitwham, Thomas Keane, Shane A McCarthy, Robert M Davies and Heng Li
_GigaScience, Volume 10, Issue 2 (2021)_ _GigaScience, Volume 10, Issue 2 (2021)_
...@@ -105,6 +123,7 @@ _GigaScience, Volume 10, Issue 2 (2021)_ ...@@ -105,6 +123,7 @@ _GigaScience, Volume 10, Issue 2 (2021)_
**Source code**: [https://github.com/samtools/samtools](https://github.com/samtools/samtools) **Source code**: [https://github.com/samtools/samtools](https://github.com/samtools/samtools)
**Documentation**: [http://samtools.sourceforge.net](http://samtools.sourceforge.net) **Documentation**: [http://samtools.sourceforge.net](http://samtools.sourceforge.net)
## Minimap2
**Minimap2: pairwise alignment for nucleotide sequences** **Minimap2: pairwise alignment for nucleotide sequences**
Heng Li Heng Li
_Bioinformatics, Volume 34, Issue 18 (2018)_ _Bioinformatics, Volume 34, Issue 18 (2018)_
...@@ -113,6 +132,7 @@ _Bioinformatics, Volume 34, Issue 18 (2018)_ ...@@ -113,6 +132,7 @@ _Bioinformatics, Volume 34, Issue 18 (2018)_
**Source code**: [https://github.com/lh3/minimap2](https://github.com/lh3/minimap2) **Source code**: [https://github.com/lh3/minimap2](https://github.com/lh3/minimap2)
**Documentation**: [https://lh3.github.io/minimap2/minimap2.html](https://lh3.github.io/minimap2/minimap2.html) **Documentation**: [https://lh3.github.io/minimap2/minimap2.html](https://lh3.github.io/minimap2/minimap2.html)
## BWA
**Fast and accurate short read alignment with Burrows-Wheeler Transform** **Fast and accurate short read alignment with Burrows-Wheeler Transform**
Heng Li and Richard Durbin Heng Li and Richard Durbin
_Bioinformatics, Volume 25, Aricle 1754-60 (2009)_ _Bioinformatics, Volume 25, Aricle 1754-60 (2009)_
...@@ -121,6 +141,7 @@ _Bioinformatics, Volume 25, Aricle 1754-60 (2009)_ ...@@ -121,6 +141,7 @@ _Bioinformatics, Volume 25, Aricle 1754-60 (2009)_
**Source code**: [https://github.com/lh3/bwa](https://github.com/lh3/bwa) **Source code**: [https://github.com/lh3/bwa](https://github.com/lh3/bwa)
**Documentation**: [http://bio-bwa.sourceforge.net](http://bio-bwa.sourceforge.net) **Documentation**: [http://bio-bwa.sourceforge.net](http://bio-bwa.sourceforge.net)
## Sickle-trim
**Sickle: A sliding-window, adaptive, quality-based trimming tool for FastQ files** **Sickle: A sliding-window, adaptive, quality-based trimming tool for FastQ files**
Joshi NA and Fass JN Joshi NA and Fass JN
_(2011) _(2011)
...@@ -129,6 +150,7 @@ _(2011) ...@@ -129,6 +150,7 @@ _(2011)
**Source code**: [https://github.com/najoshi/sickle](https://github.com/najoshi/sickle) **Source code**: [https://github.com/najoshi/sickle](https://github.com/najoshi/sickle)
**Documentation**: []() **Documentation**: []()
## Cutadapt
**Cutadapt Removes Adapter Sequences From High-Throughput Sequencing Reads** **Cutadapt Removes Adapter Sequences From High-Throughput Sequencing Reads**
Marcel Martin Marcel Martin
_EMBnet Journal, Volume 17, Article 1 (2011) _EMBnet Journal, Volume 17, Article 1 (2011)
...@@ -137,6 +159,7 @@ _EMBnet Journal, Volume 17, Article 1 (2011) ...@@ -137,6 +159,7 @@ _EMBnet Journal, Volume 17, Article 1 (2011)
**Source code**: [https://github.com/marcelm/cutadapt](https://github.com/marcelm/cutadapt) **Source code**: [https://github.com/marcelm/cutadapt](https://github.com/marcelm/cutadapt)
**Documentation**: [https://cutadapt.readthedocs.io/en/stable/](https://cutadapt.readthedocs.io/en/stable) **Documentation**: [https://cutadapt.readthedocs.io/en/stable/](https://cutadapt.readthedocs.io/en/stable)
## MultiQC
**MultiQC: summarize analysis results for multiple tools and samples in a single report** **MultiQC: summarize analysis results for multiple tools and samples in a single report**
Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
_Bioinformatics, Volume 32, Issue 19 (2016)_ _Bioinformatics, Volume 32, Issue 19 (2016)_
...@@ -145,6 +168,7 @@ _Bioinformatics, Volume 32, Issue 19 (2016)_ ...@@ -145,6 +168,7 @@ _Bioinformatics, Volume 32, Issue 19 (2016)_
**Source code**: [https://github.com/ewels/MultiQC](https://github.com/ewels/MultiQC) **Source code**: [https://github.com/ewels/MultiQC](https://github.com/ewels/MultiQC)
**Documentation**: [https://multiqc.info](https://multiqc.info) **Documentation**: [https://multiqc.info](https://multiqc.info)
## FastQ-Screen
**FastQ Screen: A tool for multi-genome mapping and quality control** **FastQ Screen: A tool for multi-genome mapping and quality control**
Wingett SW and Andrews S Wingett SW and Andrews S
_F1000Research (2018)_ _F1000Research (2018)_
...@@ -153,6 +177,7 @@ _F1000Research (2018)_ ...@@ -153,6 +177,7 @@ _F1000Research (2018)_
**Source code**: [https://github.com/StevenWingett/FastQ-Screen](https://github.com/StevenWingett/FastQ-Screen) **Source code**: [https://github.com/StevenWingett/FastQ-Screen](https://github.com/StevenWingett/FastQ-Screen)
**Documentation**: [https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen) **Documentation**: [https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen)
## FastQC
**FastQC: A quality control tool for high throughput sequence data** **FastQC: A quality control tool for high throughput sequence data**
Simon Andrews Simon Andrews
_Online (2010)_ _Online (2010)_
...@@ -161,6 +186,7 @@ _Online (2010)_ ...@@ -161,6 +186,7 @@ _Online (2010)_
**Source code**: [https://github.com/s-andrews/FastQC](https://github.com/s-andrews/FastQC) **Source code**: [https://github.com/s-andrews/FastQC](https://github.com/s-andrews/FastQC)
**Documentation**: [https://www.bioinformatics.babraham.ac.uk/projects/fastqc](https://www.bioinformatics.babraham.ac.uk/projects/fastqc) **Documentation**: [https://www.bioinformatics.babraham.ac.uk/projects/fastqc](https://www.bioinformatics.babraham.ac.uk/projects/fastqc)
## Seqtk
**Seqtk: A fast and lightweight tool for processing sequences in the FASTA or FASTQ format** **Seqtk: A fast and lightweight tool for processing sequences in the FASTA or FASTQ format**
Heng Li Heng Li
_Online (2014)_ _Online (2014)_
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