A set of Pure Data abstractions, including sequencers, GUIs, and other utilities.

Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)

Analysis pipelines for genomic sequencing data

Prophage Tracer: precisely tracing prophages in prokaryotic genomes using overlapping split-read alignment

Optimised pipeline to process whole genome sequence data from fastq to BAM on NCI Gadi

less like viewer for fastq files

Calculate fastq reads and sequencing coverage

DeepVariant-on-Spark is a germline short variant calling pipeline that runs Google DeepVariant on Apache Spark at scale.

nRex: Germline and somatic single-nucleotide, short indel and structural variant calling

This pipeline is intended to be a convenient way to work though large sets of metagenomic or metatranscriptiomic datasets while also retaining high analytical flexibility due to retained intermediate results that might be useful outside of the intended purpose.

Automated Pipeline for Variant/Haplotype Calling and Filtering

Pipeline to reconstruct the targeted dominant consensus genome of viral samples and analyze their within-host variability.

A workflow for m6A-SAC-seq data processing.

Construction of IHGV sequences from RNA-seq

🌱📦 A collection of bioinformatics tools for working with sequence data.

iMARGI-Docker distributes the iMARGI sequencing data processing pipeline

An example script of how to download WGBS data from SLIMS, check md5sums, merge lanes, and submit a project to CpG_Me

Stacks is a software pipeline for building loci from short-read sequences - Now in a Docker

Variant calling of WGS datasets