All Published Workflows
90 workflows that have been reviewed and published
V-pipe is a pipeline designed for analysing NGS data of short viral genomes
V-pipe is a workflow designed for the analysis of next generation sequencing (NGS) data from viral pathogens. It produces a n...
A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
A tool for generating bacterial genomes from metagenomes with Nanopore long read sequencing First, install miniconda3 The...
Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.
This is a complete standardized workflow the assembly and subsequent analysis for short-read viral sequencing.
This core work...
Transparent and robust SARS-CoV-2 variant calling and lineage assignment with comprehensive reporting.
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
A straightforward bioinformatic pipeline for detecting a bacterial strain in one or more metagenome(s).
A straightforward bioinformatic pipeline for detecting the presence of a bacterial strain in one or more metagenome(s). Strai...
Pipeline for Cut&Tag analysis
Snakemake pipeline for Cut&Tag analysis
# cd into a project directory
# type the following to get a copy of the pipeline
git ...
Analysis code for the TAP-seq manuscript.
This repository contains code to reproduce the results presented in the article. It builds upon a snakemake workflow that...
bigWig
ucsc-liftover
BiocParallel
Biopython
Biostrings
BSgenome
Consensus
GenomicAlignments
GenomicFeatures
GenomicRanges
HiTC
Pandas
Picard
rtracklayer
SAMtools
Snakemake
STAR
Trimmomatic
corrplot
eulerr
factoextra
GGally
ggplot2
ggpubr
ggrepel
gridExtra
here
kableExtra
Matrix
optparse
plotly
pROC
readxl
tidyverse
numpy
plotly
A Snakemake workflow for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, and GSEApy.
Given human (hg19 or hg38) or mouse (mm9 or mm10) based genomic region sets (i.e., region sets) and/or (ranked) gene sets...
A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
A tool for generating bacterial genomes from metagenomes with Nanopore long read sequencing First, install miniconda3 The...
A straightforward bioinformatic pipeline for detecting a bacterial strain in one or more metagenome(s).
A straightforward bioinformatic pipeline for detecting the presence of a bacterial strain in one or more metagenome(s). Strai...
Ultimate ATAC-seq Data Processing & Analysis Pipeline
From r A w (unaligned) BAM files to normali Z ed counts. A Snakemake implementation of the BSF's
ATAC-seq Data ...