All Published Workflows

292 workflows that have been reviewed and published

psychip_snakemake
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ENCODE pipeline for histone marks developed for the psychENCODE project
public

public

psychip pipeline is an improved version of the ENCODE pipeline for histone marks developed for the psychENCODE project. The o...
raw sequence reads Alignment Sequence alignment report macs2 ucsc-bedclip bedGraphToBigWig BEDTools BWA Picard SAMtools Snakemake
Free
74
cellranger-snakemake-gke
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snakemake workflow to run cellranger on a given bucket using gke.
public

public

A Snakemake workflow for running cellranger on a given bucket using Google Kubernetes Engine. The usage of this workflow ...
macs2 ucsc-bedclip bedGraphToBigWig BEDTools BWA Picard SAMtools Snakemake
Free
74
armor
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Light-weight Snakemake workflow for preprocessing and statistical analysis of RNA-seq data
public

public

ARMOR ( A utomated R eproducible MO dular R NA-seq) is a Snakemake workflow , aimed at performing a ty...
JSON User metadata Expression analysis Quality control report bedGraphToBigWig BEDTools Cutadapt FastQC MultiQC Quant Salmon SAMtools Snakemake STAR Trim_Galore RNA-Seq
Free
22
nanopype
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Snakemake pipelines for nanopore sequencing data archiving and processing
public

public

Detailed documentation and tutorials are available at readthedocs . Nanopype is a snakemake based pipeline providing conv...
Sample annotation Base-calling Alignment sniffles svim bedGraphToBigWig BEDTools Flye GUPPY Minimap2 nanopolish NGMLR Pandas Racon SAMtools Singularity Hub Snakemake wtdbg2 graphmap2 matplotlib numpy oschmod seaborn nanopore
Free
87
pyflow-chipseq
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a snakemake pipeline to process ChIP-seq files from GEO or in-house
public

public

a snakemake pipeline to process ChIP-seq files from GEO I have so many people asking me to process a public GEO ChIP-seq data...
Database metadata Peak calling Plot macs2 BEDTools Bowtie 2 DeepTools FastQC MultiQC Sambamba SAMBLASTER SAMtools Snakemake ChIP-seq
Free
17
dna-seq-varlociraptor
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A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse, germline, pedigree, populations) via the unified statistical model of Varlociraptor.
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public

A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse...
JSON raw sequence reads Variant calling genetic variants delly gatk rust-bio-tools snakemake-wrapper-utils tabix BCFtools BEDTools Bowtie 2 BWA Cutadapt FastQC fgbio FreeBayes mosdepth MultiQC Pandas Picard SAMtools Snakemake Variant Effect Predictor (VEP) vembrane numpy oschmod sklearn statsmodels Varlociraptor DNA
Free
127
stainedglass
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Make colorful identity heatmaps of genomic sequence
public

public

This is a repository for making colorful identity heatmaps of genomic sequence. To install you can follow the directions on t...
Sample annotation Chromatographic alignment Heat map cooler BEDTools BWA Minimap2 SAMtools Snakemake Genomics
Free
22
pyflow-atacseq
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ATAC-seq snakemake pipeline
public

public

source: http://www.the-scientist.com/?articles.view/articleNo/44772/title/Reveling-in-the-Revealed/ https://www.biostars.org/...
Expression data Peak calling Plot macs2 ataqv BEDTools Bowtie 2 DeepTools FastQC MultiQC SAMBLASTER SAMtools Snakemake ATAC-seq
Free
16
lathe
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A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
public

public

A tool for generating bacterial genomes from metagenomes with Nanopore long read sequencing First, install miniconda3 The...
bacterial Base-calling Sample annotation mummer2circos tabix BCFtools BEDTools BWA CANU Consensus Flye GUPPY Medaka Minimap2 NanoPlot pilon Racon SAMtools Snakemake pysam metagenomics
Free
39
ncov-tools
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Small collection of tools for performing quality control on coronavirus sequencing data and genomes
public

public

Tools and plots for perfoming quality control on coronavirus sequencing results. Download the package: git clone https://gith...
Sample annotation Sequencing quality control Report Augur BEDTools Pangolin SAMtools Snakemake Genomics
Free
46
covid-19-signal
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Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.
public

public

This is a complete standardized workflow the assembly and subsequent analysis for short-read viral sequencing. This core work...
FASTQ-illumina Query script Genome assembly Taxonomic classification tabix BCFtools BEDTools breseq BWA Consensus FastQC FreeBayes iVar kraken2 Pangolin QUAST SAMtools Snakemake vt Trim_Galore COVID19 Risk Mitigation
Free
31
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