Awesome Bioinformatics

A suite of utilities for converting to and working with CSV, the king of tabular file formats.

Official git repository for Biopython (originally converted from CVS)

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Repository for the CWL standards. Use https://cwl.discourse.group/ for support 😊

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

Cloud-native genomic dataframes and batch computing

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

De novo assembler for single molecule sequencing reads using repeat graphs

Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

Yet another redundant workflow engine

Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/

Efficient pythonic random access to fasta subsequences

JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.

cython + htslib == fast VCF and BCF processing

A Variant Call Format reader for Python.

Access to Biological Web Services from Python.

Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")

GFF and GTF file manipulation and interconversion

Genomic variant annotation and functional effect prediction

Bpipe - a tool for running and managing bioinformatics pipelines

Blazing-Fast Bioinformatic Operations on Python DataFrames

CGAT-ruffus is a lightweight python module for running computational pipelines

python access to UCSC genomes database

An imagemagick-like frontend to Biopython SeqIO

Simple FASTQ quality assessment using Python

Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.

Note: tabix and bgzip binaries are now part of the HTSlib project.

A simple Partial Order Aligner based on Lee, Grasso and Sharlow (2002), for education/demonstration purposes

A fast Python library for VCF files leveraging Cython for speed.

The command-line interface to GGD

📈 DNA Sequence Visualization for Humans

A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies

Write-once-read-many table for large datasets.

Explore and analyze biological sequence data

A bam toolbox