64 results found Sort:

google
deepvariant google
697
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
OpenGene
fastp OpenGene
333
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 about a month ago
broadinstitute
gatk broadinstitute
575
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
4,669 commits to master branch, last one 15 days ago
galaxyproject
galaxy galaxyproject
966
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
76,677 commits to dev branch, last one 14 hours ago
samtools
htslib samtools
448
778
other
63
C library for high-throughput sequencing data formats
bam bcf ngs sam vcf cram htslib bioinformatics
Created 2012-05-15
3,253 commits to develop branch, last one a day ago
deeptools
deepTools deeptools
204
657
other
37
Tools to process and analyze deep sequencing data.
ngs python rna-seq chip-seq genomics bioinformatics
Created 2013-07-08
3,487 commits to master branch, last one 2 months ago
flowhub-team
awesome-omics flowhub-team
63
541
mit
35
A collection of awesome things regarding all omics.
ngs omics awesome protein genomics single-cell ngs-pipeline wgs-analysis
Created 2022-02-15
216 commits to main branch, last one 4 months ago
lindenb
jvarkit lindenb
131
468
other
27
Java utilities for Bioinformatics
ngs java biology science genomics bioinformatics next-generation-sequencing
Created 2013-05-06
3,237 commits to master branch, last one 3 days ago
aidenlab
juicer aidenlab
181
393
mit
17
A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
ngs hi-c genomics 3d-genome bioinformatics 3d-genome-browser
Created 2015-12-24
402 commits to main branch, last one about a year ago
maxplanck-ie
snakepipes maxplanck-ie
85
372
mit
19
Customizable workflows based on snakemake and python for the analysis of NGS data
ngs hi-c rna-seq atac-seq chip-seq workflow snakemake bisulfite-sequencing
Created 2016-03-23
3,817 commits to master branch, last one about a month ago
bioconvert
bioconvert bioconvert
42
354
gpl-3.0
20
Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.
ngs bam2sam bcf2vcf sam2bam sniffer bam2cram cram2bam cram2sam embl2ena sequence convertor phylogeny bigbed2bed conversion embl2fasta fasta2fastq embl2genbank genbank2embl genbank2fasta bioinformatics
Created 2017-10-11
1,920 commits to main branch, last one 6 months ago
fulcrumgenomics
fgbio fulcrumgenomics
68
304
mit
20
Tools for working with genomic and high throughput sequencing data.
ngs umi fgbio scala genomics bioinformatics molecular-indexes analyzing-genomic-data
Created 2016-03-03
718 commits to main branch, last one a day ago
galaxyproject
training-material galaxyproject
850
297
mit
52
A collection of Galaxy-related training material
ngs rnaseq chip-seq training tutorial materials usegalaxy proteomics metagenomics hacktoberfest
Created 2015-06-29
25,204 commits to main branch, last one 18 hours 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
2,837 commits to master branch, last one 2 months ago
sortmerna
sortmerna sortmerna
68
230
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
ugeneunipro
ugene ugeneunipro
60
201
gpl-2.0
22
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
16,967 commits to master branch, last one 2 days ago
lgmgeo
AnnotSV lgmgeo
36
194
gpl-3.0
10
Annotation and Ranking of Structural Variation
sv cnv ngs ranking genetics annotation priorization
Created 2019-07-09
247 commits to master branch, last one 17 days ago
open2c
cooler open2c
53
191
bsd-3-clause
14
A cool place to store your Hi-C
ngs hdf5 hi-c cooler python sparse genomics 3d-genome chromatin file-format bioinformatics contact-matrix
Created 2016-01-13
1,078 commits to master branch, last one 4 days ago
hms-dbmi
scde hms-dbmi
64
171
other
25
R package for analyzing single-cell RNA-seq data
r ngs analysis single-cell heterogenity bioinformatics transcriptomics
Created 2015-05-06
157 commits to main branch, last one about a year ago
vanheeringen-lab
seq2science vanheeringen-lab
26
146
mit
6
Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.
ngs sra fastq rna-seq atac-seq chip-seq pipeline snakemake workflows bioinformatics reproducible-research bioinformatics-pipeline
Created 2019-07-11
1,483 commits to master branch, last one 3 months ago
OpenGene
MutScan OpenGene
38
145
mit
22
Detect and visualize target mutations by scanning FastQ files directly
ngs fastq cancer somatic variant mutation detection validation visualization bioinformatics
Created 2016-07-23
259 commits to master branch, last one 2 years ago
ngless-toolkit
ngless ngless-toolkit
25
143
other
11
NGLess: NGS with less work
bwa ngs fastq haskell science genomics samtools fastq-format metagenomics bioinformatics haskell-language bioinformatics-pipeline next-generation-sequencing
Created 2013-01-08
2,450 commits to main branch, last one 23 days ago
epam
cloud-pipeline epam
58
143
apache-2.0
21
Cloud agnostic genomics analysis, scientific computation and storage platform
aws ngs azure cloud biology chemistry modelling google-cloud
Created 2019-03-06
5,709 commits to develop branch, last one a day ago
sequana
sequana sequana
27
140
bsd-3-clause
7
Sequana: a set of Snakemake NGS pipelines
ngs pacbio de-novo rna-seq coverage sequanix taxonomy snakemake variant-calling
Created 2016-03-07
6,337 commits to main branch, last one 2 months ago
CRG-CNAG
CalliNGS-NF CRG-CNAG
52
130
mpl-2.0
9
GATK RNA-Seq Variant Calling in Nextflow
ngs gatk rna-seq genomics nextflow bioinformatics variant-calling
Created 2017-02-28
171 commits to master branch, last one 2 years ago
cbg-ethz
V-pipe cbg-ethz
42
127
apache-2.0
10
V-pipe is a pipeline designed for analysing NGS data of short viral genomes
hiv ngs conda virus genomics sarscov2 snakemake sars-cov-2 sequencing biohackeu20 biohackeu21 biohackeu22 biohackcovid20 bioinformatics bioinformatics-pipeline
Created 2017-04-10
1,071 commits to master branch, last one 15 hours ago
zhanxw
rvtests zhanxw
40
126
unknown
13
Rare variant test software for next generation sequencing data
ngs gwas skat umich kernel genetics genotype variants vcf-files c-plus-plus rare-variant meta-analysis association-analysis next-generation-sequencing
Created 2013-01-09
1,204 commits to master branch, last one 3 years ago
ablab
IsoQuant ablab
11
123
other
10
Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
ngs pacbio rna-seq nanopore bioinformatics transcriptomics
Created 2020-04-15
1,320 commits to master branch, last one 17 days ago
indexofire
pathongs indexofire
90
123
unknown
5
Pathogen NGS Documentary
ngs hzcdc pathogen bioinformatics genomic-epidemiology
Created 2018-05-17
152 commits to main branch, last one about a month ago
ncbi
TPMCalculator ncbi
34
122
other
20
TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files
ngs tpm rna-seq
Created 2018-03-09
155 commits to master branch, last one 3 years ago