All Published Workflows

20 workflows that have been reviewed and published

cd4-csaw
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Reproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set
public

public

This is the code for a re-analysis of a [GEO dataset][1] that I originally analyzed for [this paper][2] using statistical met...
BSgenome.Hsapiens.UCSC.hg19 BSgenome.Hsapiens.UCSC.hg38 Gene ID Peak calling Quality control report macs2 ucsc-liftover BEDTools BiocParallel Bowtie 2 csaw Cufflinks GenomicAlignments GenomicRanges GLUE graphite GSEABase HISAT2 kallisto Quant rtracklayer Salmon SAMtools Snakemake SRAdb STAR SummarizedExperiment assertthat dplyr forcats future getopt ggforce ggplot2 here ks magrittr optparse reshape2 rex rlang scales stringr rpy2 rctutils ChIP-seq
Free
114
dna-seq-benchmark
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A snakemake workflow for benchmarking variant calling approaches with Genome in a Bottle (GIAB), CHM (syndip) or other custom datasets
public

public

A Snakemake workflow for benchmarking variant calling approaches with Genome in a Bottle (GIAB) data (and other custom benchm...
JSON Gene ID Variant calling genetic variants snakemake-wrapper-utils BCFtools BEDTools BWA mosdepth Pandas Picard RTG Core SAMtools Snakemake common numpy pysam scipy sklearn statsmodels Genomics
Free
48
mirflowz
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Snakemake workflow for the mapping and quantification of miRNAs and isomiRs from miRNA-Seq libraries.
public

public

MIRFLOWZ is a [Snakemake][snakemake] workflow for mapping miRNAs and isomiRs. Installation Cloning the repos...
Gene ID Quantification Gene report gffread SAMtools Snakemake RNA-Seq
Free
58
metagenome-assembly
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Workflow module for metagenome assembly
public

public

A Snakemake workflow for metagenome assembly using metaspades and metahit. It does pre-assembly merging and read-correction i...
Gene ID Sample annotation Genome assembly Quality control report Report prodigal snakemake-wrapper-utils MEGAHIT Pandas SAMtools Snakemake SPAdes TADpole utils metagenomics
Free
19
snakemake-alignment_phylogeny
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Houses a snakemake workflow used for multiple sequence alignment and maximum likelihood phylogeny construction of genes or proteins. Originally used to study sex determination genes in mosquitoes.
public

public

This snakemake file contains a workflow allowing the creation of MAFFT alignments and RAxML phylogenies. Inputs can either be...
Gene ID Multiple sequence alignment Phylogenetic tree raxml-ng MAFFT API (EBI) Snakemake trimAl Phylogeny
Free
8
snakemake-umetaflow
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Created for testing the metabolomics pipeline through snakemake
public

public

This is the Snakemake implementation of the pyOpenMS workflow tailored by Eftychia Eva Kontou and Axel Walter ...
Gene ID Nextflow Quantification Alignment Nextflow Pandas Pyteomics Snakemake networkx numpy Gene structure
Free
6
vdblab-shotgun
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Shotgun metagenomic sequencing processing pipeline
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public

Snakemake Apptainer/Singularity : while in many cases we do provide conda envs the only method of execution we...
Gene ID Gene prediction Gene report ABRicate AMRFinderPlus antismash-lite bracken hmmer antiSMASH BBMap Bowtie 2 cloudSPAdes CoverM dbCAN2 FastQC humann kraken2 Krona MetaErg MetaPhlAn MetaQUAST metaspades MetaWRAP plasmidspades QUAST rnaspades SAMtools seqkit Snakemake SortMeRNA SPAdes RGI Metagenomic sequencing
Free
3
downstream_isoseq_process
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process aligned isoseq libraries to: 1. identify consensus gene models ; 2. compare gene model maintenance between samples
public

public

This is a Snakemake project template. The Snakefile is under workflow . Slides describing and justifying the use ...
Gene ID Analysis Report BEDTools Biopython GenomicRanges GLUE IsoSeq3 Minimap2 orfipy Pandas SAMtools seqkit seqtk Snakemake subSeq ggplot2 tidyverse Function analysis
Free
46
use-public-resources-to-answer-a-biological-questi
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Use Public Resources to answer a biological question
public

public

How to access genomic resource via its Python API How to access image resource via its Python API Relate image data to ...
JSON Gene ID Analysis Image InterMine Pandas ipywidgets matplotlib numpy omero-py requests skimage Gene expression
Free
39
pox-virus-amplicon-main
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Pox Virus Illumina Amplicon Workflow for half-genomes sequencing data
public

public

This workflow generates consensus sequences from Illumina PE-sequenced ARTIC data of pox virus samples. It requires that all ...
Gene ID Read mapping Genome map Galaxy illumina biotools:tada-amplicon WorkflowHub Data identity and mapping
Free
vgp-hybrid-scaffolding-with-bionano-optical-maps
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VGP hybrid scaffolding with Bionano optical maps
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public

Performs scaffolding using Bionano Data. Part of VGP assembly pipeline.
Gene ID Sequencing quality control Plot BUSCO Galaxy QUAST WorkflowHub Sequence assembly
Free
vgp-purge-assembly-with-purge_dups-pipeline
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VGP purge assembly with purge_dups pipeline
public

public

Purge Phased assembly of duplications and overlaps. Include purge steps for Primary and Alternate assemblies.
Gene ID Sequencing quality control Plot BUSCO Galaxy QUAST WorkflowHub Sequence assembly
Free