Update v.2022.11

config/config.yaml

@@ -49,13 +49,17 @@ conda:
 
 ### FASTQSCREEN --------------------------------------------------------------------------------------
 fastq-screen:
-  config: 'config/fastq-screen.conf' # Path to the fastq-screen configuration file
+  config: 'config/fastq-screen_bwa.conf' # Path to the fastq-screen configuration file
+  # Available options:
+    #- 'config/fastq-screen_bwa.conf'     # Default fastq-screen configuration file for bwa users
+    #- 'config/fastq-screen_bowtie2.conf' # Default fastq-screen configuration file for bowtie2 users
+    #- 'config/fastq-screen_custom.conf'  # Your cutom fastq-screen configuration file
   subset: 10000                      # Don't use whole sequences, but a subset reads (default: "1000") [INT] (0=all)
   mapper: 'bwa'                      # Mapper used by fastq-screen for alignments (default "bwa")
   # Available options:
-    #- 'bwa'     # Burrows-Wheeler Aligner (default, somme small genomes indexes provided, see "fastq-screen.conf")
-    #- 'bowtie'  # Bowtie (indexes not provided for fastq-screen)
-    #- 'bowtie2' # Bowtie2 (indexes not provided for fastq-screen)
+    #- 'bwa'     # Burrows-Wheeler Aligner (default, somme small genomes indexes provided, see "fastq-screen_bwa.conf")
+    #- 'bowtie2' # Bowtie2                 (somme small genomes indexes provided, see "fastq-screen_bowtie2.conf")
+    #- 'bowtie'  # Bowtie                  (indexes not provided for fastq-screen)
 
 ### BWA ----------------------------------------------------------------------------------------------
 bwa:

config/fastq-screen_bowtie2.conf

+###I###R###D######U###2###3###3#######T###R###A###N###S###V###I###H###M###I####
+# Name ___________________ fastq-screen.conf
+# Version ________________ v.2022.11
+# Author _________________ Nicolas Fernandez
+# Affiliation ____________ IRD_TransVIHMI
+# Aim ____________________ Configuration file for Fastq-Screen (with bowtie2)
+# Date ___________________ 2021.04.30
+# Latest modifications ___ 2022.11.18
+# Use ____________________ Edit default settings (and add fasta reference)
+
+###############################################################################
+
+#### MOLECULAR BIOLOGY SEQUENCES ----------------------------------------------------------------------------
+
+### PhiX - QC_phi-X174_Coliphage_NC-001422.1
+DATABASE	PhiX		resources/indexes/bowtie2/QC_phi-X174_Coliphage_NC-001422-1
+### Kanamycin - Kanamycin-Resistance-Gene
+DATABASE      	Kanamycin	resources/indexes/bowtie2/QC_Kanamycin-Resistance-Gene
+### Adapters - QC_NGS-Adapters (FastQC contaminants: www.bioinformatics.babraham.ac.uk/projects/fastqc)
+DATABASE	Adapters	resources/indexes/bowtie2/QC_NGS-adapters
+### Vectors - QC_UniVec_wo_PhiX_and_Kanamycin (UniVec database: http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html) without PhiX and Kanamycin
+DATABASE	Vectors	resources/indexes/bowtie2/QC_UniVec_wo_phiX_and_kanamycin
+
+#### TRANSVIHMI ORGANISMS -----------------------------------------------------------------------------------
+
+#### Putative Hosts  (Large genomes) -----
+
+### Gorilla g4
+#DATABASE	Gorilla	resources/indexes/bowtie2/Gorilla_gorilla_g4
+### Chimpanzee t3
+#DATABASE    Chimpanzee	resources/indexes/bowtie2/Pan_troglodytes_t3
+### Human - HOST_Homo-sapiens_h38_NC-000001.11
+#DATABASE	Human	resources/indexes/bowtie2/HOST_Homo-sapiens_h38_NC-000001-11
+### Bat v1
+#DATABASE	Bat	resources/indexes/bowtie2/Pteropus_vampyrus_v1
+
+#### Main Viruses (Small genomes) -----
+
+### SARS-CoV-2 - SARS-CoV-2_Wuhan_MN908947.3
+DATABASE	SARS-CoV-2	resources/indexes/bowtie2/SARS-CoV-2_Wuhan_MN908947-3
+### MPXV - Monkeypox-virus_Zaire_AF380138.1
+DATABASE	Monkeypox	resources/indexes/bowtie2/Monkeypox-virus_Zaire_AF380138-1
+### SPXV - Swinepox-virus_India_MW036632.1
+DATABASE	Swinepox	resources/indexes/bowtie2/Swinepox-virus_India_MW036632-1
+### EBOV - Ebola-virus_Zaire_AF272001.1
+DATABASE	Ebola		resources/indexes/bowtie2/Ebola-virus_Zaire_AF272001-1
+### HIV - HIV-1_HXB2_K03455.1
+DATABASE	HIV		resources/indexes/bowtie2/HIV-1_HXB2_K03455-1
+
+#### LAB MODEL ORGANISMS ------------------------------------------------------------------------------------
+
+### E. coli (Bacteria) - QC_Echerichia-coli_CP060121.1
+DATABASE	Ecoli 	  resources/indexes/bowtie2/QC_Echerichia-coli_CP060121-1
+### S. cerevisiae (Yeast) - sequence
+#DATABASE	  Scerevisiae	resources/indexes/bowtie2/Saccharomyces_cerevisiae
+### C. elegans (Nematode) - sequence
+#DATABASE	  Celegans	resources/indexes/bowtie2/Caenorhabditis_elegans
+### D. melanogaster (Fruit fly) - sequence
+#DATABASE	  Dmelanogaster	resources/indexes/bowtie2/Drosophila_melanogaster
+### D. rerio (Zebrafish) - sequence
+#DATABASE  Drerio      resources/indexes/bowtie2/Danio_rerio
+### X. laevis (Xenope) - sequence
+#DATABASE   Xlaevis  resources/indexes/bowtie2/Xenopus_laevis
+### G. gallus - sequence
+#DATABASE  Ggallus	ressources/indexes/bowtie2/Gallus_gallus
+### Mouse m39
+#DATABASE	Mouse	 resources/indexes/bowtie2/Mus_musculus_m39
+### Arabidopsis t10 (Plant) - sequence from NCBI (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/735/GCF_000001735.3_TAIR10/GCF_000001735.3_TAIR10_genomic.fna.gz)
+#DATABASE	Arabidopsis	 resources/indexes/bowtie2/Arabidopsis_thaliana_t10

config/fastq-screen.conf → config/fastq-screen_bwa.conf

@@ -5,7 +5,7 @@
 # Affiliation ____________ IRD_TransVIHMI
 # Aim ____________________ Configuration file for Fastq-Screen (with bwa)
 # Date ___________________ 2021.04.30
-# Latest modifications ___ 2022.11.10
+# Latest modifications ___ 2022.11.18
 # Use ____________________ Edit default settings (and add fasta reference)
 
 ###############################################################################

workflow/rules/indexing_genomes.smk

@@ -4,7 +4,7 @@
 # Affiliation ____________ IRD_U233_TransVIHMI
 # Aim ____________________ Snakefile with indexing genomes rules
 # Date ___________________ 2022.09.28
-# Latest modifications ___ 2022.11.10
+# Latest modifications ___ 2022.11.18
 # Use ____________________ snakemake -s indexing_genomes.smk --use-conda 
 
 ###############################################################################

workflow/rules/quality_control.smk

@@ -4,7 +4,7 @@
 # Affiliation ____________ IRD_U233_TransVIHMI
 # Aim ____________________ Snakefile with quality control rules
 # Date ___________________ 2021.09.28
-# Latest modifications ___ 2022.11.10
+# Latest modifications ___ 2022.11.18
 # Run ____________________ snakemake -s quality_control.smk --use-conda 
 
 ###############################################################################