All Published Workflows

110 workflows that have been reviewed and published

natrix
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Open-source bioinformatics pipeline for the preprocessing of raw sequencing data.
public

public

Natrix is an open-source bioinformatics pipeline for the preprocessing of raw sequencing data. The need for a scalable, repro...
raw sequence reads Primer removal Quality control report dada2 BLAST cd-hit Cutadapt FastQC MultiQC Pandas PANDAseq seqtk ShortRead Snakemake Swarm VSEARCH AmpliconDuo data.table ggplot2 xtable dinopy numpy PyYAML tables Function analysis
Free
44
mapache
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mapping pipeline for ancient DNA
public

public

Mapache ([maˈpa.t͡ʃe]) is a lightweight mapping pipeline for ancient DNA using the workflow manager Snakemake . Visit ...
BAM Sample ID Mapping Report gatk tabix AdapterRemoval BCFtools BEDTools Bowtie 2 BWA fastp FastQC gatk_realigner_target_creator MapDamage MultiQC Pandas Picard QualiMap SAMtools seqtk Snakemake GLIMPSE numpy Comparative genomics
Free
95
metax_bakeoff_2019
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Metagenomic Taxonomic Classification Benchmarking Workflow
public

public

Metagenomic taxonomic classification benchmarking This package is contains snakemake workflows, a jupyter notebook and a pyth...
raw sequence reads Taxonomic classification Taxonomy bracken prophyle BLAST Centrifuge Diamond FastQC Kaiju Kraken kraken2 metaX Picard SAMtools seqtk Snakemake ncbi-genome-download metagenomics
Free
78
mof-search
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BLAST-like search across all pre-2019 bacteria on ordinary laptop and desktop computers within a few hours
public

public

Introduction Citation Installation Step 1: Install dependencies Step 2: Clone the re...
seqtk Snakemake
Free
12
kount
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Snakemake pipeline calculating KEGG orthologue abundance in metagenomic sequence data.
public

public

Snakemake pipeline calculating KEGG orthologue abundance in metagenomic sequence data. KOunt is a Snakemake pipeline that cal...
Pathway ID (KEGG) Quantification Quality control report prodigal MEGAHIT BEDTools BWA cd-hit Diamond fastp kallisto MMseqs Quant SAMtools seqtk Snakemake subSeq kofam_scan oschmod metagenomics
Free
41
oecophylla
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Modular Shotgun Sequence Analysis Workflow: Oecophylla - Harnessing Snakemake
public

public

Canonically pronounced ee-co-fill-uh , Oecophylla is a Snakemake wrapper for shotgun sequence analysis. Rather than being...
raw sequence reads Analysis Sequence report scp MEGAHIT Anvio BEDTools Bowtie 2 Centrifuge FastQC HUMAnN2 Kraken Mash MetaQUAST MultiQC Pandas QUAST SAMtools seqtk Snakemake SPAdes SqueezeMeta numpy scikit-bio Sequence analysis
Free
48
nbis-meta
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A snakemake workflow for metagenomic projects
public

public

A workflow for metagenomic projects A snakemake workflow for paired- and/or single-end whole-genome shotgun metagenomic d...
Barrnap prodigal MEGAHIT Biopython BLAST Bowtie 2 Centrifuge CheckM contigtax Cutadapt edgeR eggNOG-mapper v2 FastANI FastQC FeatureCounts Infernal cmscan (EBI) kraken2 Krona MaxBin MetaBAT 2 metagenomeSeq MetaPhlAn metaspades MultiQC Pandas Picard SAMtools seqtk Snakemake SortMeRNA SqueezeMeta Trimmomatic Trnascan-SE CONCOCT common gtdbtk networkx numpy RGI
Free
137
ameta
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Ancient microbiome snakemake workflow
public

public

aMeta is a Snakemake workflow for identifying microbial sequences in ancient DNA shotgun metagenomics samples. The workflow p...
pmdtools AMPS Bowtie 2 Cutadapt FastQC KrakenUniq Krona MapDamage MultiQC SAMtools seqtk Snakemake subSeq Malt
Free
31
mag_snakemake_wf
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Recovery of prokaryotic genomes from shotgun metagenomic sequencing data
public

public

Overview System Requirements Workflow setup Running pipeline CPU time License ...
scp Bowtie 2 BWA CheckM CRIMSON dRep FastQC Mash metaprokka MetaWRAP MultiQC SAMtools seqtk Snakemake SPAdes SRA ggplot2 gridExtra RColorBrewer tidyr gtdbtk
Free
74
pacman-pipeline
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Bioinformatics pipeline for the analysis of amplicon sequencing data of eDNA samples from the PacMAN project
public

public

This is the bioinformatics pipeline developed for the PacMAN (Pacific Islands Marine Bioinvasions Alert Network). This pipeli...
JSON dada2 Biopython Biostrings BLAST Bowtie 2 Cutadapt FastQC MultiQC phyloseq seqtk Snakemake subSeq Trimmomatic dplyr ggplot2 plyr stringr tibble tidyr worrms xml2 yaml
Free
27
gavisunk
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Genome Assembly Validation via Inter-SUNK distances in ONT reads
public

public

Genome Assembly Validation via Inter-SUNK distances in nanopore reads Setup source files in config.yaml and ont.tsv config.ya...
rustybam BEDTools Jellyfish mrsFAST Pandas PyRanges SAMtools seqtk Snakemake graph-tool matplotlib ncls networkx numpy scipy seaborn
Free
29
phytopipe
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Plant Pathogen Detection Pipeline (PhytoPipe) for RNA-seq Data
public

public

# PhytoPipe: A Phytosanitary Pipeline for plant pathogen detection and diagnosis using RNA-seq data PhytoPipe is an open-sour...
RNA sequence Sequence read processing Sequence report bwakit crass Bowtie 2 BWA cloudSPAdes metaspades MultiQC MUMmer4 plasmidspades QUAST rnaspades RVDB-prot seqtk Snakemake SPAdes Trimmomatic Plant biology RNA-Seq
Free
1