Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines...
Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform
Flexible circular visualization of genome-associated data with BioPerl and SVG.
Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files. It's a lightweight wrapper of...
Python wrapper -- and more -- for Aaron Quinlan's BEDTools (bioinformatics tools)
Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl
tools for adding mutations to existing .bam files, used for testing mutation callers
A set of tools written in Perl and C++ for working with VCF files, such as...
a simple C++ library for parsing and manipulating VCF files, + many command-line utilities
This is the official development repository for BCFtools. To compile, the develop branch of htslib is...
SAMStat displays various properties of next-generation sequencing reads stored in SAM/BAM format.
Tools (written in C using htslib) for manipulating next-generation sequencing data
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to...
A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin
Easily submitting multiple PBS jobs or running local jobs in parallel. Multiple input files supported.