All Published Workflows

112 workflows that have been reviewed and published

armor
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Light-weight Snakemake workflow for preprocessing and statistical analysis of RNA-seq data
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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
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
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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
pipeline-transcriptome-de
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Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
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This project is deprecated. Please see our newer wf-transcriptomes , which contains functionality for differential exp...
FASTQ Sample ID Alignment Count matrix Minimap2 Quant Salmon SAMtools Snakemake stageR dplyr ggplot2 tidyr Gene expression
Free
14
rna-seq-kallisto-sleuth
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A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
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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
uncovar
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Transparent and robust SARS-CoV-2 variant calling and lineage assignment with comprehensive reporting.
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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
cd4-csaw
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Reproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set
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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
rna-seq-pop
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Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data
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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
eukrhythmic
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A metatranscriptomic pipeline optimized for the study of microeukaryotes.
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This README file is a brief introduction to eukrhythmic . For more detailed information, please visit the readthedo...
FASTQ Sample annotation Transcriptome assembly Quality control report BBMap BEDTools cd-hit Quant QUAST Salmon Snakemake TransDecoder metagenomics
Free
27
kount
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Snakemake pipeline calculating KEGG orthologue abundance in metagenomic sequence data.
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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
iguide
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Bioinformatic pipeline for identifying dsDNA breaks by marker based incorporation, such as breaks induced by designer nucleases like Cas9.
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Bioinformatic pipeline for processing iGUIDE and GUIDE-seq samples. iGUIDE is a pipeline written in snakemake for proc...
Data Read pre-processing Report Biostrings BSgenome BWA Quant SAMtools Snakemake magrittr DNA
Free
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dna-seq-neoantigen-prediction
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Neoantigen Prediction Snakemake Workflow: Genomic Variant Detection and Peptidome Incorporation
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This workflow detects genomic variants with Strelka and and tries to incorporate germline and somatic variants into a sam...
Sequence Genetic variation analysis genetic variants gatk hla-la rust-bio-tools tabix Arriba BCFtools BWA Cutadapt FreeBayes kallisto Microphaser NetMHCIIpan NetMHCpan Pandas Picard Quant razers3 SAMtools Snakemake STAR Strelka Variant Effect Predictor (VEP) vembrane Jinja2 numpy Varlociraptor Genomics
Free
122
filtar
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Using RNA-Seq data to improve microRNA target prediction accuracy in animals
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FilTar is a tool to integrate RNA-Seq data to pre-existing miRNA target prediction workflows in order to increase prediction ...
miranda BEDTools Biopython gtftogenepred HISAT2 Quant Salmon SAMtools Snakemake tidyverse oschmod Trim_Galore
Free
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