All Published Workflows

5 workflows that have been reviewed and published

snake_gtdbtk
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A snakemake for GTDB-tk
public

public

It uses GTDB-tk to taxonomically annotate your genomes and to build a tree. Run as follows: dbdir="databases" genome_dir="gen...
Database metadata Genome annotation Phylogenetic tree Pandas Snakemake ete3 gtdbtk numpy utils Phylogeny
Free
10
gatk-snakemake-pipeline
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DNA-seq and Neoantigens prediction
public

public

Snakemake workflow for neoantigen prediction. This workflow is still in development This snakemake pipeline implement...
JSON Sample annotation Genome annotation Genome report gatk BWA fastp Picard razers3 SAMtools Snakemake DNA Genomics
Free
28
bactprep
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Flexible workflow designed for bacterial WGS analyses (annotation, core/pan-genome reconstruction, phylogeny)
public

public

This pipeline is written specifically for annotating the bacteria whole genome sequences (WGS) . The pipeline handles mul...
Gene identifier Genome annotation Annotation track BEDTools Biopython IQ-TREE metaprokka Pandas PIRATE Roary seqkit Snakemake snippy matplotlib pyLabLib Phylogeny
Free
40
indelcoordinatecorrection
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Snakemake workflow: InDelCoordinateCorrection
public

public

A Snakemake workflow to correct genome annotation feature coordinates after polishing a reference genome using short reads fr...
Genome annotation Sequence coordinate conversion snakemake-wrapper-utils Bwa-mem2 Pandas Picard pilon SAMtools Snakemake Trim_Galore Sequence analysis
Free
16
mgnify-genomes-analysis-pipeline
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MGnify genomes analysis pipeline
public

public

MGnify genomes analysis pipeline MGnify A pipeline to perform taxonomic and functional annotation and to generate a catal...
FASTQ raw sequence reads Genome annotation genetic variants AMRFinderPlus bracken gunc CheckM Diamond dRep eggNOG-mapper v2 Infernal cmscan (EBI) InterProScan (EBI) IQ-TREE kraken2 Mash metaprokka MMseqs Nextflow SAMtools seqtk subSeq Trnascan-SE cmsearch extglob gtdbtk taxonomic and functional annotation
Free
53