Fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs. [ paper-2020 ]
NimMIT Licenseactive
Awesome Bioinformatics
Search 121 Bioinformatics projects →121 projects31 categoriesshowing 61–120, page 2 of 3
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- 16%steady
- 21%slowing
- 28%dormant
Sourced fromdanielecook/Awesome-Bioinformatics
Projects 61–120 of 121, most starred first
Python wrapper for bedtools. [ paper-2011 | web ]
PythonOtherslowing
A polymorphic bayesian genotyping model with wide applicability. [ paper-2021 ]
C++MIT Licensesteady
Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. [ paper-2010 ]
C++Boost Software License 1.0dormant
International association of users & developers of open source Perl tools for bioinformatics, genomics and life sciences. [ paper-2002 | web ]
Perlactive
GFF and GTF file manipulation and interconversion. [ web ]
PythonMIT Licensesteady
A collection of research papers for AI-based protein design.
Apache License 2.0slowing
Modular and universal bioinformatics, Bionode provides pipeable UNIX command line tools and JavaScript APIs for bioinformatics analysis workflows. [ web ]
JavaScriptMIT Licensesteadyarchived
Genetic variant annotation and effect prediction toolbox. [ paper-2012 | web ]
JavaOthersteady
Variant Discovery in High-Throughput Sequencing Data. [ web ]
Javadormant
Comes with samtools! - Reads simulator. [ web ]
Cdormant
SIMD C library for global, semi-global, and local pairwise sequence alignments [ paper-2016 ]
COthersteady
GRIDSS: the Genomic Rearrangement IDentification Software Suite. [ paper-2017 ]
JavaOtherslowing
JavaScript library that can be used to generate interactive and highly customizable web-based genome browsers. [ paper-2016 ]
JavaScriptApache License 2.0dormant
Syntax Highlighting for Computational Biology file formats (SAM, VCF, GTF, FASTA, PDB, etc...) in vim/less/gedit/sublime. [ paper-2018 | web ]
ShellGNU General Public License v3.0dormant
structural variant calling and genotyping with existing tools, but,smoothly.
GoApache License 2.0slowing
Tools for adding mutations to existing .bam files, used for testing mutation callers. [ web ]
PythonMIT Licenseactive
A small language for defining pipeline stages and linking them together to make pipelines. [ web ]
GroovyOtheractive
Embeddable genome viewer. Integration data from a wide variety of sources, and can load data directly from popular genomics file formats including bigWig, BAM, and VCF. [ paper-2011 | web ]
JavaScriptBSD 2-Clause "Simplified" Licensedormant
Easily get SRA download links and other information. [ web ]
HTMLGNU General Public License v2.0slowing
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data. [ paper-2017 ]
PythonMIT Licensedormant
FASTQ/A short-reads pre-processing tools: Demultiplexing, trimming, clipping, quality filtering, and masking utilities. [ web ]
COtherdormant
A compressor of common genomic file formats (BAM, CRAM, FASTQ, VCF etc). [ web | paper-2021 ]
COtheractive
Python library for blazing-fast genomic interval operations and genomic file formats I/O on Polars DataFrames [ paper-2025 | [ web ] ]
PythonApache License 2.0active
Scalable gVCF merging and joint variant calling for population sequencing projects. [ paper-2018 ]
C++Apache License 2.0slowing
Computation Pipeline library for python widely used in science and bioinformatics. [ paper-2010 | web ]
PythonMIT Licensedormant
Pythonic access to the UCSC Genome database. [ paper-2013 ]
PythonMIT Licensedormant
Sequence manipulation toolkit for FASTA/FASTQ files written in Nim. [ paper-2021 | web ]
NimGNU General Public License v3.0active
SKESA is a de-novo sequence read assembler for microbial genomes. It uses conservative heuristics and is designed to create breaks at repeat regions in the genome. This leads to excellent sequence quality without significantly compromising contiguity.
C++Otherslowing
Biocaml aims to be a high-performance user-friendly library for Bioinformatics.
OCamlOthersteady
file format conversion in Biopython in a convenient way. [ web ]
PythonGNU General Public License v3.0slowing
A generic but comprehensive bacterial annotation pipeline, built with Nextflow, with nice graphical options for investigating results. [ web ]
NextflowGNU General Public License v3.0steady
FASTQ and SAM quality control using Python.
PythonMIT Licensesteady
A circos representation of multiple GWAS results. [ paper-2018 ]
RGNU General Public License v3.0slowing
Table file index. [ paper-2011 ]
Cdormantarchived
A cross-system scripting language for working with big data pipelines in computer systems of different sizes and capabilities. [ paper-2014 | web ]
Shelldormant
Perl package for circular plots, which are well suited for genomic rearrangements. [ paper-2009 | web ]
Perldormant
A wee tool for random access into BGZF files.
CMIT Licensedormant
Telseq is a tool for estimating telomere length from whole genome sequence data. [ paper-2014 ]
C++GNU General Public License v3.0dormant
Partial-Order Alignment for fast alignment and consensus of multiple homologous sequences. [ paper-2002 ]
PythonGNU General Public License v3.0slowing
JavaScript library for drawing canvas-based gene diagrams. [ paper-2012 | web ]
JavaScriptdormant
Horizon chart D3-based JavaScript library for DNA data. [ paper-2016 | web ]
CSSOtherdormant
Fast FASTQ filtering by matching reads against one or more regex patterns.
RustMIT Licensesteady
List of resources on alternative splicing including software, databases, and other tools.
dormant
A port of pyVCF using Cython for speed.
PythonMIT Licensedormant
Flexible circular visualization of genome-associated data with BioPerl and SVG. [ paper-2014 ]
PerlOtherdormant
Go Get Data; A command line interface for obtaining genomic data. [ web ]
PythonMIT Licensedormant
Sort genomic files according to a specified order.
GoMIT Licensesteady
A pipeline for preprocessing short and long sequencing reads, built with Nextflow. [ web ]
NextflowGNU General Public License v3.0slowing
D3 JavaScript based genome viewer. Constructs SVGs. [ paper-2015 ]
JavaScriptGNU General Public License v2.0dormant
Hadoop Oozie-based workflow system focused on genomics data analysis in cloud environments. [ paper-2010 | web ]
JavaGNU General Public License v3.0dormant
Easily submitting PBS jobs with script template. Multiple input files supported.
PythonMIT Licensedormant
Write-once-read-many table for large datasets.
PythonGNU Lesser General Public License v3.0slowing
BWA-MEM drop-in replacement: 2-3x faster, 2-5x cheaper, 100% identical output on standard CPUs. [ paper-2026 ]
CMIT Licensesteady
Workflow standard developed by the Broad. [ web ]
JavaBSD 3-Clause "New" or "Revised" Licensedormantarchived
Displaying sequence statistics for next-generation sequencing. [ paper-2010 | web ]
COtherdormant
UNIX-style FASTA manipulation tools.
PythonMIT Licenseslowing
Point and click, cross platform suite for analysing and visualizing next-generation sequencing datasets. [ paper-2018 | web ]
TypeScriptGNU General Public License v3.0dormant
Automate common SAM & BAM conversions.
Pythondormant
Customizable pipeline for differential expression analysis with an intuitive GUI. [ web ]
JavaOtherdormant