All Published Workflows

353 workflows that have been reviewed and published

psychip_snakemake
Show Details View Workflow
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
Show Details View Workflow
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
rna-seq-star-deseq2
Show Details View Workflow
RNA-seq workflow using STAR and DESeq2
public

public

This workflow performs a differential gene expression analysis with STAR and Deseq2. The usage of this workflow is described ...
raw sequence reads Gene expression profiling ID list snakemake-wrapper-utils biomaRt PCAtools BiocParallel BWA Cutadapt DESeq2 GFFutils MultiQC Pandas SAMtools Snakemake STAR cli stringr tidyverse RNA-Seq
Free
41
dna-seq-gatk-variant-calling
Show Details View Workflow
This Snakemake pipeline implements the GATK best-practices workflow
public

public

This Snakemake pipeline implements the GATK best-practices workflow for calling small germline variants. The usage of thi...
VCF raw sequence reads Variant calling genetic variants gatk rust-bio-tools snakemake-wrapper-utils tabix BCFtools BWA FastQC MultiQC Pandas Picard SAMtools Snakemake Trimmomatic Variant Effect Predictor (VEP) common matplotlib numpy seaborn DNA
Free
57
metagem
Show Details View Workflow
: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
v-pipe
Show Details View Workflow
V-pipe is a pipeline designed for analysing NGS data of short viral genomes
public

public

V-pipe is a workflow designed for the analysis of next generation sequencing (NGS) data from viral pathogens. It produces a n...
Sample annotation Primer removal Quality control report bcl2fastq-nextseq consensusfixer demultiplexer indelfixer Augur BWA Consensus iVar lofreq Pandas SAMtools Snakemake Vicuna numpy PyVCF scikit-bio scipy Genomics
Free
68
dna-seq-varlociraptor
Show Details View Workflow
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.
public

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
rna-seq-kallisto-sleuth
Show Details View Workflow
A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
public

public

A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth . The usage of thi...
JSON Expression data Expression analysis Expression data bioawk snakemake-wrapper-utils biomaRt IHW Biopython BWA CPAT Cutadapt fgsea graphite GSEA IsoformSwitchAnalyzeR kallisto limma Pandas pheatmap Picard Quant SAMtools sleuth Snakemake SPIA dplyr fs ggplot2 ggpubr gridExtra tidyr tidyverse altair altair-saver goatools matplotlib numpy pysam scipy RNA-Seq
Free
105
stainedglass
Show Details View Workflow
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
lathe
Show Details View Workflow
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
covid-19-signal
Show Details View Workflow
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
pore-c-snakemake
Show Details View Workflow
Pore-C Snakemake Workflow for Processing and Analysis of Nanopore Sequencing Data
public

public

This pipeline manages a pore-c workflow starting from raw fastq files and converting them to standard file formats for use by...
raw sequence reads Alignment Feature table cooler BWA Pairix SAMtools Snakemake Sequence analysis
Free
32