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Awesome Bioinformatics
Search 121 Bioinformatics projects →121 projects31 categories
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- 16%steady
- 21%slowing
- 28%dormant
Sourced fromdanielecook/Awesome-Bioinformatics
Projects 1–60 of 121, most starred first
A list of pipeline resources.
active
Utilities for working with CSV/Tab-delimited files. [ web ]
PythonMIT Licenseactive
Freely available tools for biological computing in Python, with included cookbook, packaging and thorough documentation. Part of the Open Bioinformatics Foundation. Contains the very useful Entrez package for API access to the NCBI databases. [ paper-2009 | web ]
PythonOtheractive
Deep learning-based variant caller [ paper-2018 ]
PythonBSD 3-Clause "New" or "Revised" Licensesteady
(recommended) - A fluent DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner. [ paper-2018 | web ]
GroovyApache License 2.0active
Scalable toolkit for analyzing single-cell gene expression data, including preprocessing, visualization, clustering, and trajectory inference. [ paper-2018 | web ]
PythonBSD 3-Clause "New" or "Revised" Licenseactive
Minimap2 is an pairwise aligner for genomic and spliced nucleotide sequences. It can perform the assembly-to-assembly alignment, and works with gzip'd FASTQ, FASTA formats. It also finds overlaps between long-reads.
COtheractive
Ultra-fast, sensitive search and clustering suite for protein and nucleotide sequence sets. [ paper-2017 | paper-2018 ]
CMIT Licenseactive
Git repo of useful single line commands.
slowing
Rust implementations of algorithms and data structures useful for bioinformatics. [ paper-2016 ]
RustMIT Licenseactive
Burrow-Wheeler Aligner for pairwise alignment between DNA sequences.
CGNU General Public License v3.0active
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang. [ paper-2016 | web ]
GoMIT Licenseactive
Toolkit for processing sequences in FASTA/Q formats.
CMIT Licenseslowing
a specification for describing analysis workflows and tools that are portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and high performance computing (HPC) environments. [ web ]
Common Workflow LanguageApache License 2.0active
Educational resource on performing RNA-seq analysis in the cloud using Amazon AWS cloud services. Topics include preparing the data, preprocessing, differential expression, isoform discovery, data visualization, and interpretation.
ROtherdormant
An ultrafast protein aligner for blastp and blastx like searches. [ paper-2021 ]
C++GNU General Public License v3.0active
Another cross-platform, efficient, practical and pretty CSV/TSV toolkit. [ web ]
GoMIT Licenseactive
Workflow library embedded in the Go programming language, focusing on supporting complex workflow constructs, compiling to a single binary, providing powerful file naming and comprehensive audit reports for every output [ paper-2019 | web ]
GoMIT Licenseslowing
@crazyhottommy's notes on various steps and considerations when doing RNA-seq analysis.
PythonMIT Licensedormant
A Workflow Management System geared towards scientific workflows. [ web ]
ScalaBSD 3-Clause "New" or "Revised" Licenseactive
Scalable genomic analysis.
PythonMIT Licenseactive
A Swiss Army knife for genome arithmetic. [ paper-2010 | paper-2014 | web ]
CMIT Licenseactive
Prokka: rapid prokaryotic genome annotation. Prokka is one of the most cited annotation command line tools for microbial genome annotations.
PerlGNU General Public License v3.0steady
SPAdes (St. Petersburg genome assembler) is an assembly toolkit containing various assembly pipelines and the de-facto standard for prokaryotic genome assemblies.
C++Otheractive
Python wrapper for samtools. [ web ]
CythonMIT Licenseactive
samtools/bcftools are a suite of tools for manipulating NGS data and can be used to call variants. [ paper-2009 | web ]
COtheractive
fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing. [ paper-2017 ]
NimMIT Licensesteady
Resources on ChIP-seq data which include papers, methods, links to software, and analysis.
PythonMIT Licenseslowing
An ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. [ paper-2012 | web ]
C++GNU General Public License v3.0active
A haplotype-resolved assembler for accurate Hifi reads.
C++MIT Licenseactive
Java-based browser. Fast, efficient, scalable visualization tool for genomics data and annotations. Handles a large variety of formats. [ paper-2019 | web ]
JavaMIT Licenseactive
A single molecule sequence assembler for genomes large and small.
C++active
A C++ library for parsing and manipulating VCF files.
C++MIT Licensesteady
Bakta is a tool for the rapid & standardized annotation of bacterial genomes & plasmids. It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis.
PythonGNU General Public License v3.0active
Create an index on a compressed text file.
CBSD 2-Clause "Simplified" Licensedormant
Java framework for processing biological data.
JavaGNU Lesser General Public License v2.1active
A quality control tool for high throughput sequence data. [ web ]
JavaGNU General Public License v3.0active
A python-based workflow manager.
PythonApache License 2.0active
Suite of tools to handle gene annotations in any GTF/GFF format. [ web ]
HTMLGNU General Public License v3.0steady
A system for rapidly aligning entire genomes, whether in complete or draft form. [ paper-1999 | paper-2002 | paper-2004 | web ]
C++Artistic License 2.0slowing
VCF manipulation and statistics (e.g. linkage disequilibrium, allele frequency, Fst). [ paper-2011 ]
C++GNU Lesser General Public License v3.0slowing
Predicts whether an amino acid substitution affects protein function. [ paper-2003 | web ]
MIT Licenseslowing
A fuzzy Bruijn graph approach to long noisy reads assembly
CGNU General Public License v3.0slowing
Structural variant discovery by integrated paired-end and split-read analysis. [ paper-2012 ]
C++BSD 3-Clause "New" or "Revised" Licenseactive
A flexible pipeline, built with Nextflow, for the complete analysis of bacterial genomes. [ web ]
NextflowMIT Licenseactive
BioJS is a library of over hundred JavaScript components enabling you to visualize and process data using current web technologies. [ paper-2014 | web ]
Apache License 2.0dormant
Expertly curated genomics papers to get up to speed on genomics, RNA-seq, statistics (used in genomics), software development, and more.
dormant
Pythonic access to FASTA files.
PythonOthersteady
A software package for estimating gene and isoform expression levels from RNA-Seq data. [ paper-2011 | web ]
C++GNU General Public License v3.0active
JavaScript genome browser that is highly customizable via plugins and track customizations. [ paper-2016 | web ]
JavaScriptOtheractive
Structural variant and indel caller for mapped sequencing data. [ paper-2015 ]
C++Othersteadyarchived
The modern C++ library for sequence analysis.
C++Otheractive
Cython + HTSlib == fast VCF parsing; even faster parsing than pyVCF. [ paper-2017 | web ]
CythonMIT Licenseactive
Collection of tools for working with BAM files. [ paper-2011 ]
C++MIT Licenseslowing
A VCF Parser for Python. [ web ]
PythonOtherslowing
Pythonic Access to the Ensembl database. [ web ]
PythonApache License 2.0active
Annotate a VCF with other VCFs/BEDs/tabixed files. [ paper-2016 ]
GoMIT Licenseactive
lumpy: a general probabilistic framework for structural variant discovery. [ paper-2014 ]
CMIT Licensesteady
Access to Biological Web Services from Python. [ paper-2013 web ]
PythonOtheractive