All Published Workflows

229 workflows that have been reviewed and published

metagem
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:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
public

public

Note An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic inte...
JSON raw sequence reads Genome assembly Quality control report prodigal MEGAHIT BWA CheckM fastp kallisto MaxBin memote MetaBAT 2 metaprokka MetaWRAP Quant Roary SAMtools Snakemake SqueezeMeta CONCOCT carve gtdbtk smetana metagenomics
Free
35
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
snparcher
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Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.
public

public

snpArcher is a reproducible workflow optimized for nonmodel organisms and comparisons across datasets, built on the Snakema...
CleanEx dataset code Variant calling Quality control report gatk genmap tabix BCFtools BEDTools BWA fastp mosdepth Picard Sambamba SAMtools Sentieon DNASeq Snakemake Data quality management
Free
40
assembly-annotation-pipeline
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Plant genome assembly and annotation pipeline using snakemake
public

public

This Snakemake pipeline aims for plant genome assembly with HiFi data and genome annotation with RNA-Seq/IsoSeq. Modified fro...
Genome index Annotation Map BEDTools BLAST fastp FastQC GFF3 Rebase gffread HISAT2 Minimap2 RepeatMasker RepeatModeler SAMtools Snakemake StringTie RNA-Seq
Free
20
uncovar
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Transparent and robust SARS-CoV-2 variant calling and lineage assignment with comprehensive reporting.
public

public

A reproducible and scalable workflow for transparent and robust SARS-CoV-2 variant calling and lineage assignment with com...
JSON raw sequence reads Variant calling genetic variants delly nanofilt rust-bio-tools snakemake-wrapper-utils tabix BCFtools Biopython BWA CANU Consensus fastp FastQC fgbio FreeBayes GFFutils kallisto Kraken Krona Medaka metaspades Minimap2 MultiQC Pandas Pangolin Picard Quant QUAST SAMtools Snakemake Variant Effect Predictor (VEP) vembrane altair intervaltree numpy pysam requests Varlociraptor COVID19 Risk Mitigation
Free
204
stag-mwc
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StaG Metagenomic Workflow Collaboration
public

public

The StaG Metagenomic Workflow Collaboration (mwc) project focuses on providing a metagenomics analysis workflow suitable for ...
JSON bracken BBMap Bowtie 2 fastp FeatureCounts humann Kaiju Kraken kraken2 KrakenUniq Krona MetaPhlAn MultiQC Pandas SAMtools Singularity Hub Snakemake matplotlib numpy seaborn
Free
78
rna-seq-pop
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Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data
public

public

Documentation : https://sanjaynagi.github.io/rna-seq-pop/ Walkthrough : https://www.youtube.com/watch?v=5QQe7DLHO4...
FASTQ-illumina JSON Sample annotation Variant calling genetic variants snakemake-wrapper-utils EnhancedVolcano BCFtools DESeq2 fastp FreeBayes GLUE HISAT2 kallisto mosdepth MultiQC Pandas pheatmap Quant SAMBLASTER SAMtools sleuth Snakemake snpEff Vcflib data.table dplyr ggplot2 ggrepel jsonlite openxlsx RColorBrewer tidyverse ipykernel matplotlib matplotlib-venn numpy papermill pop-tools scipy zarr Population genomics
Free
63
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
cuttag-pipeline
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Pipeline for Cut&Tag analysis
public

public

Snakemake pipeline for Cut&Tag analysis # cd into a project directory # type the following to get a copy of the pipeline git ...
preseq ucsc-bigwigmerge ucsc-bigwigtobedgraph PCAtools bedGraphToBigWig BEDTools Bowtie 2 Consensus DeepTools DESeq2 fastp FastQC MultiQC Pandas pheatmap plyranges Sambamba SAMtools Snakemake vsn dendextend ggplot2 ggrepel gplots PoiClaClu RColorBrewer tidyr tidyverse plotly
Free
28
genome-seek
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Clinical Whole Genome Sequencing Pipeline
public

public

Whole Genome Clinical Sequencing Pipeline. This is the home of the pipeline, genome-seek. Its long-term goals: to ac...
gatk hla-la peddy tabix AnnotSV BCFtools Bowtie 2 Bwa-mem2 fastp FastQC gatk_realigner_target_creator MultiQC NG-Circos octopus Pandas Picard QualiMap SAMBLASTER SAMtools Singularity Hub Snakemake VCFtools GLnexus
Free
57
snakemake_chipseq_pe
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Pipeline for the analysis of PE ChIP-seq data
public

public

Snakemake pipeline made for reproducible analysis of paired-end Illumina ChIP-seq data. The desired output of this pipelin...
macs2 Bowtie 2 DeepTools fastp SAMtools Snakemake Trimmomatic
Free
21
vgea
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VGEA (Viral Genomes Easily Analyzed) is a pipeline for analysis of RNA virus next-generation sequencing data.
public

public

VGEA (Viral Genomes Easily Analyzed) is an RNA viral assembly toolkit. VGEA was developed to aid in the analysis of next gene...
BWA fastp MultiQC QUAST SAMtools seqkit Snakemake
Free
12