69 results found Sort:

google
deepvariant google
698
3.1k
bsd-3-clause
159
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
dna ngs genome science genomics sequencing tensorflow deepvariant deep-learning bioinformatics machine-learning deep-neural-network
Created 2017-11-23
2,374 commits to r1.6.1 branch, last one 2 months ago
bitfieldaudio
OTTO bitfieldaudio
143
2.6k
other
209
Sampler, Sequencer, Multi-engine synth and effects - in a box! [WIP]
audio music synth ui-design sequencing synthesizer raspberry-pi audio-processing
Created 2017-02-21
1,241 commits to develop branch, last one about a year ago
OpenGene
fastp OpenGene
334
1.8k
mit
50
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
qc ngs umi fastq polyg filter adapter merging overlap quality illumina trimming filtering splitting sequencing duplication preprocessing bioinformatics quality-control
Created 2017-10-31
448 commits to master branch, last one 2 months ago
broadinstitute
gatk broadinstitute
578
1.6k
other
156
Official code repository for GATK versions 4 and up
dna ngs gatk spark genome science genomics sequencing bioinformatics
Created 2014-12-02
4,673 commits to master branch, last one 8 days ago
galaxyproject
galaxy galaxyproject
967
1.3k
other
69
Data intensive science for everyone.
dna ngs science genomics pipeline workflow usegalaxy sequencing hacktoberfest bioinformatics workflow-engine
Created 2015-02-23
76,938 commits to dev branch, last one 23 hours ago
ablab
spades ablab
130
701
other
32
SPAdes Genome Assembler
illumina sequencing genome-assembly sequence-assembler metagenome-assembly transcriptome-assembly next-generation-sequencing
Created 2016-06-01
15,097 commits to next branch, last one 9 days ago
brentp
mosdepth brentp
99
667
mit
23
fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
nim wgs depth exome genome coverage nim-lang sequencing hacktoberfest
Created 2017-08-24
230 commits to master branch, last one about a month ago
xebia-functional
fetch xebia-functional
49
495
apache-2.0
52
Simple & Efficient data access for Scala and Scala.js
cats data monix scala monads scala-js sequencing concurrency parallelism data-fetching
Created 2016-03-04
1,343 commits to main branch, last one 22 days ago
ideoforms
isobar ideoforms
51
357
mit
19
A Python library for creating and manipulating musical patterns, designed for use in algorithmic composition, generative music and sonification. Can be used to generate MIDI events, MIDI files, OSC me...
midi music sequencing composition algorithmic-composition
Created 2011-08-04
524 commits to master branch, last one 2 months ago
milaboratory
mixcr milaboratory
78
311
other
30
MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
10x t-cell rep-seq rna-seq antibody immunology sequencing single-cell bioinformatics t-cell-receptor
Created 2015-03-30
3,668 commits to develop branch, last one 14 days ago
sanger-pathogens
Roary sanger-pathogens
189
301
other
29
Rapid large-scale prokaryote pan genome analysis
genomics pathogen research sequencing global-health bioinformatics infectious-diseases bioinformatics-pipeline next-generation-sequencing
Created 2013-04-18
930 commits to master branch, last one 2 years ago
ACEnglish
truvari ACEnglish
47
297
mit
14
Structural variant toolkit for VCFs
vcf genomics sequencing sv-merging benchmarking data-science bioinformatics vcf-comparison annotation-tool structural-variation
Created 2018-04-13
1,297 commits to develop branch, last one 24 days ago
r3fang
SnapATAC r3fang
125
294
gpl-3.0
14
Analysis Pipeline for Single Cell ATAC-seq
sequencing epigenetics single-cell-analysis single-cell-atac-seq bioinformatics-pipeline machine-learning-algorithms
Created 2019-02-19
228 commits to master branch, last one 2 years ago
tmhglnd
mercury tmhglnd
13
277
gpl-3.0
12
A minimal and human-readable language and environment for the live coding of algorithmic electronic music.
osc sounds mercury visuals language livecoding sequencing live-coding performance creative-coding mercury-environment algorithmic-composition human-readable-language
Created 2019-11-19
625 commits to master branch, last one 14 days ago
samtools
htsjdk samtools
244
274
unknown
49
A Java API for high-throughput sequencing data (HTS) formats.
bam dna ngs sam vcf cram java fasta genomics java-api sequencing
Created 2014-04-29
2,838 commits to master branch, last one 8 days ago
wurmlab
sequenceserver wurmlab
112
267
agpl-3.0
19
Intuitive graphical web interface for running BLAST bioinformatics tool (i.e. have your own custom NCBI BLAST site!)
ruby blast genomics javascript sequencing hacktoberfest visualization bioinformatics sequence-alignment genomics-visualization
Created 2010-10-01
2,283 commits to master branch, last one 3 days ago
biocommons
hgvs biocommons
94
233
apache-2.0
20
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
genomics variation sequencing bioinformatics genome-analysis variant-analysis
Created 2017-03-09
1,653 commits to main branch, last one 9 days ago
sortmerna
sortmerna sortmerna
69
232
gpl-3.0
14
SortMeRNA: next-generation sequence filtering and alignment tool
cpp ngs python alignment sequencing bioinformatics metatranscriptomics
Created 2014-03-14
1,335 commits to master branch, last one about a month ago
sanger-pathogens
Artemis sanger-pathogens
74
229
other
17
Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation
genomics pathogen research sequencing global-health bioinformatics infectious-diseases bioinformatics-pipeline next-generation-sequencing
Created 2009-09-30
5,443 commits to master branch, last one about a year ago
sanger-pathogens
circlator sanger-pathogens
56
219
other
21
A tool to circularize genome assemblies
genomics pathogen research sequencing global-health bioinformatics infectious-diseases bioinformatics-pipeline next-generation-sequencing
Created 2015-04-16
387 commits to master branch, last one 9 months ago
ZJUFanLab
scCATCH ZJUFanLab
36
205
gpl-3.0
4
Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
seurat rna-seq sequencing single-cell cell-markers marker-genes transcriptome transcriptomics cluster-annotation
Created 2019-08-06
118 commits to master branch, last one about a year ago
ugeneunipro
ugene ugeneunipro
60
203
gpl-2.0
21
UGENE is free open-source cross-platform bioinformatics software
cpp dna msa ngs qt5 ugene science pipeline workflow sequencing bioinformatics cross-platform
Created 2016-03-11
16,975 commits to master branch, last one 2 days ago
nextstrain
nextclade nextstrain
58
202
mit
18
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
dna rna ncov clade covid virus clades strain covid19 science covid-19 neherlab research influenza sequences nextstrain sars-cov-2 sequencing coronavirus next-generation-sequencing
Created 2020-06-12
6,213 commits to master branch, last one 17 hours ago
igordot
genomics igordot
54
190
unknown
6
A collection of scripts and notes related to genomics and bioinformatics
dna gtf vcf fast5 fasta fastq science genomics illumina nanopore workflow sequencing bioinformatics
Created 2015-12-22
115 commits to master branch, last one about a year ago
HadrienG
InSilicoSeq HadrienG
32
173
mit
10
:rocket: A sequencing simulator
sequencing simulation metagenomics bioinformatics illumina-sequencing
Created 2016-11-16
644 commits to master branch, last one 3 months ago
LooseLab
readfish LooseLab
30
161
gpl-3.0
14
CLI tool for flexible and fast adaptive sampling on ONT sequencers
ont genomics sequencing bioinformatics oxford-nanopore adaptive-sampling
Created 2019-11-08
400 commits to main branch, last one about a month ago
nickjcroucher
gubbins nickjcroucher
49
157
gpl-2.0
13
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
genomics pathogen research sequencing global-health bioinformatics infectious-diseases bioinformatics-pipeline next-generation-sequencing
Created 2011-11-01
2,418 commits to master branch, last one 5 days ago
sanger-pathogens
ariba sanger-pathogens
52
156
other
22
Antimicrobial Resistance Identification By Assembly
genomics pathogen research sequencing global-health bioinformatics infectious-diseases bioinformatics-pipeline next-generation-sequencing
Created 2015-02-11
1,797 commits to master branch, last one about a year ago
mlin
GenomicSQLite mlin
10
155
apache-2.0
5
Genomics Extension for SQLite
sqlite sqlite3 genomics sequencing bioinformatics
Created 2020-05-26
173 commits to main branch, last one 5 months ago
tobiasrausch
alfred tobiasrausch
12
134
bsd-3-clause
9
BAM Statistics, Feature Counting and Annotation
alfred quality sequencing insert-size read-counts quality-control feature-counting alignment-metrics coverage-distribution
Created 2016-02-25
763 commits to main branch, last one about a month ago