All Published Workflows

47 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
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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
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v-pipe
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V-pipe is a pipeline designed for analysing NGS data of short viral genomes
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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
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natrix
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Open-source bioinformatics pipeline for the preprocessing of raw sequencing data.
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Natrix is an open-source bioinformatics pipeline for the preprocessing of raw sequencing data. The need for a scalable, repro...
raw sequence reads Primer removal Quality control report dada2 BLAST cd-hit Cutadapt FastQC MultiQC Pandas PANDAseq seqtk ShortRead Snakemake Swarm VSEARCH AmpliconDuo data.table ggplot2 xtable dinopy numpy PyYAML tables Function analysis
Free
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snparcher
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Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.
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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
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40
chipseq
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ChIP-seq peak-calling, QC and differential analysis pipeline (Snakemake port of the nextflow pipeline at https://nf-co.re/chipseq).
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This is the template for a new Snakemake workflow. Replace this text with a comprehensive description covering the purpose an...
Data Peak calling Quality control report bedGraphToBigWig BEDTools BiocParallel BWA Cutadapt DESeq2 FastQC FeatureCounts GFFutils homer MaCS MultiQC Pandas pheatmap Picard SAMtools Snakemake UpSetR vsn ggplot2 lattice optparse RColorBrewer reshape2 scales tidyverse pysam PyYAML smart-open ChIP-seq
Free
117
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
single-cell-nanopore
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Workflow for Nanopore Sequencing of 10x single cell libraries
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ScNapBar (single-cell Nanopore barcode demultiplexer) is a workflow to assign barcodes to long-read single-cell sequencing...
Sample annotation Sequencing quality control Quality control report BEDTools Minimap2 Pandas SAMtools Snakemake caret e1071 stringdist numpy scipy nanopore
Free
31
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
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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
snakernaseq
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A Snakemake workflow to process paired-end RNA-Seq data.
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A Snakemake workflow to process paired-end RNA-Seq data. The workflow consists following steps: Quality control of th...
raw sequence reads Quantification Quality control report BWA FastQC gffread GFFutils HTSeq htseqcount kallisto MultiQC QualiMap Quant RSEM Salmon SAMtools Snakemake STAR Trim_Galore Gene expression
Free
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salmon_deseq2_snakemake
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This repository has snakemake scripts for salmon-deseq2 pipeline for RNAseq data analysis
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RNAseq data analysis by Salmon-DESeq2 and Salmon-Wasabi-Sleuth pipelines are available here. RNAseq Data is availble from G...
FASTQ Data Quantification Quality control report PCAtools tximport apeglm Cutadapt DESeq2 FastQC MultiQC pheatmap Quant regionReport Salmon sleuth Snakemake vsn ggplot2 readr stringr RNA-Seq
Free
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