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Awesome Bioinformatics
A curated list of awesome Bioinformatics libraries and software.
danielecook/Awesome-Bioinformatics
#awesome
#awesome-list
#bioinformatics
- List stars
- 4,329
- README repos
- 132
- Indexed repos
- 127
- List commits
- 273
- Forks
- 742
- Open issues
- 46
Tracked list growth
GitHub stars and default-branch commits for danielecook/Awesome-Bioinformatics.
Latest scan 2026-10-22 10:49
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Default branch commits
Latest repo push 2026-10-22
wireservice/csvkit
A suite of utilities for converting to and working with CSV, the king of tabular file formats.
- Updated
- 2026-09-21
- Lists
- 3 list mentions
- First commit
- 2011-04-01
- License
- MIT
- Issues
- 49 open
6,416
stars
- Forks
- 697
- Commits
- 2,085 commits
- Star growth, last 7 days
- +1 0.0%
- Commit velocity, last 7 days
- 0 0.0%
biopython/biopython
Official git repository for Biopython (originally converted from CVS)
GitHub topics
- Updated
- 2026-10-22
- Lists
- 2 list mentions
- First commit
- 1999-12-08
- License
- NOASSERTION
- Issues
- 634 open
5,241
stars
- Forks
- 1,976
- Commits
- 16,369 commits
- Star growth, last 7 days
- +6 +0.1%
- Commit velocity, last 7 days
- +3 0.0%
google/deepvariant
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
GitHub topics
- Updated
- 2026-09-30
- Lists
- 1 list mention
- First commit
- 2017-12-01
- License
- BSD-3-Clause
- Issues
- 8 open
3,824
stars
- Forks
- 806
- Commits
- 3,378 commits
- Star growth, last 7 days
- 0 0.0%
- Commit velocity, last 7 days
- 0 0.0%
scverse/scanpy
Single-cell analysis in Python. Scales to >100M cells.
GitHub topics
- Updated
- 2026-10-22
- Lists
- 1 list mention
- First commit
- 2017-01-29
- License
- BSD-3-Clause
- Issues
- 557 open
2,592
stars
- Forks
- 800
- Commits
- 3,912 commits
- Star growth, last 7 days
- 0 0.0%
- Commit velocity, last 7 days
- 0 0.0%
crazyhottommy/RNA-seq-analysis
RNAseq analysis notes from Ming Tang
Stack
GitHub topics
- Updated
- 2021-11-15
- Lists
- 1 list mention
- First commit
- 2015-08-26
- License
- MIT
- Issues
- 1 open
1,097
stars
- Forks
- 325
- Commits
- 322 commits
- Star growth, last 7 days
- 0 0.0%
- Commit velocity, last 7 days
- 0 0.0%
hail-is/hail
Cloud-native genomic dataframes and batch computing
AI dev
- Updated
- 2026-10-21
- Lists
- 1 list mention
- First commit
- 2015-07-24
- License
- MIT
- Issues
- 399 open
1,080
stars
- Forks
- 266
- Commits
- 12,281 commits
- Star growth, last 7 days
- 0 0.0%
- Commit velocity, last 7 days
- 0 0.0%
bcbio/bcbio-nextgen
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
- Updated
- 2024-08-24
- Lists
- 2 list mentions
- First commit
- 2010-07-24
- License
- MIT
- Issues
- 133 open
1,031
stars
- Forks
- 354
- Commits
- 8,579 commits
- Star growth, last 7 days
- 0 0.0%
- Commit velocity, last 7 days
- 0 0.0%
crazyhottommy/ChIP-seq-analysis
ChIP-seq analysis notes from Ming Tang
Stack
GitHub topics
- Updated
- 2024-08-05
- Lists
- 1 list mention
- First commit
- 2015-06-12
- License
- MIT
- Issues
- 0 open
- Forks
- 305
- Commits
- 364 commits
- Star growth, last 7 days
- 0 0.0%
- Commit velocity, last 7 days
- 0 0.0%
oschwengers/bakta
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
GitHub topics
- Updated
- 2026-10-11
- Lists
- 1 list mention
- First commit
- 2020-01-15
- License
- GPL-3.0
- Issues
- 29 open
686
stars
- Forks
- 88
- Commits
- 1,104 commits
- Star growth, last 7 days
- 0 0.0%
- Commit velocity, last 7 days
- 0 0.0%
insitro/redun
Yet another redundant workflow engine
GitHub topics
- Updated
- 2026-07-17
- Lists
- 1 list mention
- First commit
- 2021-10-08
- License
- Apache-2.0
- Issues
- 34 open
605
stars
- Forks
- 53
- Commits
- 511 commits
- Star growth, last 7 days
- 0 0.0%
- Commit velocity, last 7 days
- 0 0.0%
mdshw5/pyfaidx
Efficient pythonic random access to fasta subsequences
- Updated
- 2026-10-21
- Lists
- 1 list mention
- First commit
- 2013-09-12
- License
- NOASSERTION
- Issues
- 3 open
489
stars
- Forks
- 80
- Commits
- 938 commits
- Star growth, last 7 days
- 0 0.0%
- Commit velocity, last 7 days
- 0 0.0%
jamescasbon/PyVCF
A Variant Call Format reader for Python.
- Updated
- 2023-09-22
- Lists
- 1 list mention
- First commit
- 2011-07-23
- License
- NOASSERTION
- Issues
- 100 open
420
stars
- Forks
- 193
- Commits
- 521 commits
- Star growth, last 7 days
- 0 0.0%
- Commit velocity, last 7 days
- 0 0.0%
openvax/pyensembl
Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl
AI dev
- Updated
- 2026-10-21
- Lists
- 1 list mention
- First commit
- 2014-04-14
- License
- Apache-2.0
- Issues
- 4 open
410
stars
- Forks
- 74
- Commits
- 803 commits
- Star growth, last 7 days
- 0 0.0%
- Commit velocity, last 7 days
- 0 0.0%
cokelaer/bioservices
Access to Biological Web Services from Python.
- Updated
- 2026-06-12
- Lists
- 1 list mention
- First commit
- 2012-11-28
- License
- NOASSERTION
- Issues
- 5 open
347
stars
- Forks
- 70
- Commits
- 1,521 commits
- Star growth, last 7 days
- 0 0.0%
- Commit velocity, last 7 days
- 0 0.0%
daler/pybedtools
Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")
- Updated
- 2026-08-26
- Lists
- 1 list mention
- First commit
- 2010-05-14
- License
- NOASSERTION
- Issues
- 17 open
330
stars
- Forks
- 108
- Commits
- 1,899 commits
- Star growth, last 7 days
- 0 0.0%
- Commit velocity, last 7 days
- 0 0.0%
daler/gffutils
GFF and GTF file manipulation and interconversion
- Updated
- 2026-10-21
- Lists
- 1 list mention
- First commit
- 2011-09-18
- License
- MIT
- Issues
- 22 open
321
stars
- Forks
- 82
- Commits
- 768 commits
- Star growth, last 7 days
- 0 0.0%
- Commit velocity, last 7 days
- 0 0.0%
adamewing/bamsurgeon
tools for adding mutations to existing .bam files, used for testing mutation callers
AI dev
- Updated
- 2026-08-05
- Lists
- 1 list mention
- First commit
- 2012-05-10
- License
- MIT
- Issues
- 42 open
253
stars
- Forks
- 87
- Commits
- 647 commits
- Star growth, last 7 days
- 0 0.0%
- Commit velocity, last 7 days
- 0 0.0%
OpenGene/AfterQC
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
Stack
GitHub topics
- Updated
- 2020-05-14
- Lists
- 1 list mention
- First commit
- 2015-08-04
- License
- MIT
- Issues
- 28 open
214
stars
- Forks
- 50
- Commits
- 200 commits
- Star growth, last 7 days
- 0 0.0%
- Commit velocity, last 7 days
- 0 0.0%
biodatageeks/polars-bio
Blazing-Fast Bioinformatic Operations on Python DataFrames
AI dev
GitHub topics
- Updated
- 2026-10-21
- Lists
- 2 list mentions
- First commit
- 2024-11-26
- License
- Apache-2.0
- Issues
- 52 open
205
stars
- Forks
- 35
- Commits
- 302 commits
- Star growth, last 7 days
- 0 0.0%
- Commit velocity, last 7 days
- 0 0.0%
cgat-developers/ruffus
CGAT-ruffus is a lightweight python module for running computational pipelines
- Updated
- 2026-10-16
- Lists
- 1 list mention
- First commit
- 2009-04-29
- License
- MIT
- Issues
- 27 open
174
stars
- Forks
- 34
- Commits
- 1,317 commits
- Star growth, last 7 days
- 0 0.0%
- Commit velocity, last 7 days
- 0 0.0%
brentp/cruzdb
python access to UCSC genomes database
- Updated
- 2020-08-27
- Lists
- 1 list mention
- First commit
- 2011-09-02
- License
- MIT
- Issues
- 13 open
138
stars
- Forks
- 41
- Commits
- 177 commits
- Star growth, last 7 days
- 0 0.0%
- Commit velocity, last 7 days
- 0 0.0%
fhcrc/seqmagick
An imagemagick-like frontend to Biopython SeqIO
- Updated
- 2024-03-18
- Lists
- 1 list mention
- First commit
- 2010-12-07
- License
- GPL-3.0
- Issues
- 16 open
121
stars
- Forks
- 22
- Commits
- 515 commits
- Star growth, last 7 days
- 0 0.0%
- Commit velocity, last 7 days
- 0 0.0%
mdshw5/fastqp
Simple FASTQ quality assessment using Python
GitHub topics
- Updated
- 2026-02-24
- Lists
- 1 list mention
- First commit
- 2013-09-23
- License
- MIT
- Issues
- 13 open
111
stars
- Forks
- 15
- Commits
- 194 commits
- Star growth, last 7 days
- 0 0.0%
- Commit velocity, last 7 days
- 0 0.0%
ljdursi/poapy
A simple Partial Order Aligner based on Lee, Grasso and Sharlow (2002), for education/demonstration purposes
- Updated
- 2024-06-20
- Lists
- 1 list mention
- First commit
- 2015-04-28
- License
- GPL-3.0
- Issues
- 0 open
77
stars
- Forks
- 12
- Commits
- 48 commits
- Star growth, last 7 days
- 0 0.0%
- Commit velocity, last 7 days
- 0 0.0%
arq5x/cyvcf
A fast Python library for VCF files leveraging Cython for speed.
- Updated
- 2018-03-27
- Lists
- 1 list mention
- First commit
- 2012-04-12
- License
- MIT
- Issues
- 12 open
54
stars
- Forks
- 14
- Commits
- 84 commits
- Star growth, last 7 days
- 0 0.0%
- Commit velocity, last 7 days
- 0 0.0%
gogetdata/ggd-cli
The command-line interface to GGD
- Updated
- 2022-10-16
- Lists
- 1 list mention
- First commit
- 2016-04-22
- License
- MIT
- Issues
- 4 open
43
stars
- Forks
- 3
- Commits
- 524 commits
- Star growth, last 7 days
- 0 0.0%
- Commit velocity, last 7 days
- 0 0.0%
IQTLabs/squiggle
📈 DNA Sequence Visualization for Humans
Archived
GitHub topics
- Updated
- 2021-07-10
- Lists
- 1 list mention
- First commit
- 2018-07-04
- License
- MIT
- Issues
- 7 open
41
stars
- Forks
- 9
- Commits
- 191 commits
- Star growth, last 7 days
- 0 0.0%
- Commit velocity, last 7 days
- 0 0.0%
shenwei356/easy_qsub
Easily submitting multiple PBS jobs or running local jobs in parallel. Multiple input files supported.
- Updated
- 2023-05-24
- Lists
- 1 list mention
- First commit
- 2015-03-09
- License
- MIT
- Issues
- 1 open
29
stars
- Forks
- 8
- Commits
- 32 commits
- Star growth, last 7 days
- 0 0.0%
- Commit velocity, last 7 days
- 0 0.0%
wormtable/wormtable
Write-once-read-many table for large datasets.
- Updated
- 2023-10-05
- Lists
- 1 list mention
- First commit
- 2012-10-27
- License
- LGPL-3.0
- Issues
- 11 open
27
stars
- Forks
- 5
- Commits
- 540 commits
- Star growth, last 7 days
- 0 0.0%
- Commit velocity, last 7 days
- 0 0.0%
incertae-sedis/smof
Explore and analyze biological sequence data
GitHub topics
- Updated
- 2024-08-01
- Lists
- 1 list mention
- First commit
- 2014-04-27
- License
- MIT
- Issues
- 0 open
19
stars
- Forks
- 3
- Commits
- 583 commits
- Star growth, last 7 days
- 0 0.0%
- Commit velocity, last 7 days
- 0 0.0%
DarwinAwardWinner/mergesam
Automate common sam & bam conversions
Stack
- Updated
- 2013-04-25
- Lists
- 1 list mention
- First commit
- 2011-07-31
- License
- Unknown
- Issues
- 0 open
- Forks
- 1
- Commits
- 20 commits
- Star growth, last 7 days
- 0 0.0%
- Commit velocity, last 7 days
- 0 0.0%
AndersenLab/bam-toolbox
A bam toolbox
- Updated
- 2024-07-30
- Lists
- 1 list mention
- First commit
- 2015-10-28
- License
- MIT
- Issues
- 0 open
- Forks
- 1
- Commits
- 49 commits
- Star growth, last 7 days
- 0 0.0%
- Commit velocity, last 7 days
- 0 0.0%