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MIVEGEC / dainat / MaLBEC - Conda
Creative Commons Attribution 4.0 InternationalMaterials for Learning Bioinformatics and Enhancing Competencies - Conda
Topics: CondaUpdated -
DIADE / culebront_pipeline
GNU General Public License v3.0 or laterdojo snakemake assemblage long reads
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TRANSVIHMI / nfernandez / GeVarLi
GNU Affero General Public License v3.0GeVarLi pipeline for AFROSCREEN ANRS
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US191 / CRDAP
GNU General Public License v3.0 onlyCruise Repository for Data Acquisition and Processing
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PHIM / RNAja-pipeline
GNU General Public License v3.0 or laterUpdated -
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A, still very experimental, R package that acts as a storage location for functions and interfaces in connection with genomics (genomes, transcriptomes, annotation, phylogenomics, ...)
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PHIM / sravel / PodiumASM
MIT LicenseLong-read sequencing is a highly accurate approach that can be used to challenging genomes, such as those containing stretches of highly repetitive elements and lot of structural variant. Long read sequencing can also be used to generate de novo assembly and genome finishing applications Lot of tools are used to make genome assembly with long reads every day and sometimes you don't know wich Assembler tool is the best for your organism. PodiumASM is here for you ! PodiumASM is is an open-source, scalable, modulable and traceable snakemake pipeline, able to compare multiple long read assemblies obtained from multiple assemblers tools. The workflow PodiumASM can help you to choose the best assemblies among all possibilities.
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DIADE / Recombination_landscape / Biparental LC-NGS Snakemake
GNU Affero General Public License v3.0Updated -
TRANSVIHMI / nfernandez / Reads_Quality_Control
GNU Affero General Public License v3.0Reads Quality Control (RQC) allow raw NGS reads quality control, before continue with more downstream analysis.
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TRANSVIHMI / nfernandez / SLAM
GNU Affero General Public License v3.0SLURM Lightweight Automated Manager
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PHIM / sravel / RattleSNP
GNU General Public License v3.0 or latersnakemake workflow for mappind single/paired datas
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PHIM / acomte / RNAja
GNU General Public License v3.0 or laterUpdated -
PHIM / sravel / DNAnnot
GNU General Public License v3.0 or laterThis pipeline is an automatic structural annotation workflows written in snakemake. The annotation is based on two tools which uses RNA-Seq and/or protein homology information for predict coding sequence. One of this tools is BRAKER which use GeneMark-EX and AUGUSTUS. And the other tool is AUGUSTUS alone for improve annotation of small coding sequences with few or no intron. Before the annotation, the repeat element of genome are masked for avoid annotation probleme. In addition this workflows can perform a illumina assembly with ABySS using différent value of kmere.
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