37 results found Sort:

tanghaibao
jcvi tanghaibao
189
779
bsd-2-clause
36
Python library to facilitate genome assembly, annotation, and comparative genomics
blast allmaps synteny assembly genomics genetic-maps bioinformatics variant-calling genome-sequencing sequence-alignments comparative-genomics
Created 2010-12-01
3,045 commits to main branch, last one 41 minutes ago
vcflib
vcflib vcflib
221
629
mit
40
C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
genomics genotyping haplotypecaller variant-calling vcf-manipulation
Created 2010-09-22
1,525 commits to master branch, last one about a month ago
tseemann
snippy tseemann
117
488
gpl-2.0
30
:scissors: :zap: Rapid haploid variant calling and core genome alignment
vcf snps haploid bacteria genomics bioinformatics fastq-analysis indel-discovery variant-calling
Created 2014-05-15
421 commits to master branch, last one 5 months ago
nf-core
sarek nf-core
417
414
mit
135
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
conda gatk4 cancer nf-core somatic genomics germline nextflow pipeline workflow annotation containers target-panels bioinformatics pre-processing variant-calling reproducible-research whole-exome-sequencing whole-genome-sequencing next-generation-sequencing
Created 2019-04-30
7,940 commits to master branch, last one 23 days ago
luntergroup
octopus luntergroup
37
305
mit
19
Bayesian haplotype-based mutation calling
phasing genomics variants haplotypes single-cell bioinformatics variant-calling de-novo-mutation somatic-variants
Created 2015-02-04
5,045 commits to develop branch, last one about a year ago
HKU-BAL
Clair3 HKU-BAL
31
250
unknown
11
Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
pacbio genomics illumina nanopore ont-data long-reads ont-models deep-learning variant-calling variant-detection computational-biology
Created 2021-03-30
601 commits to main branch, last one 23 days ago
kishwarshafin
pepper kishwarshafin
42
245
mit
10
PEPPER-Margin-DeepVariant
nanopore variants long-reads pacbio-ccs oxford-nanopore variant-calling genome-variation assembly-polishing
Created 2019-05-10
1,281 commits to r0.8 branch, last one 2 years ago
suhrig
arriba suhrig
50
229
other
14
Fast and accurate gene fusion detection from RNA-Seq data
star cancer rna-seq fusion-gene gene-fusion fusion-genes gene-fusions variant-calling virus-integration structural-variation
Created 2017-10-23
694 commits to master branch, last one about a year ago
nanoporetech
megalodon nanoporetech
30
198
other
21
Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network output...
guppy basecalling epigenetics variant-calling
Created 2019-06-20
1,149 commits to master branch, last one about a year ago
atks
vt atks
3
194
mit
13
A tool set for short variant discovery in genetic sequence data.
variant-calling
Created 2013-10-03
1,333 commits to master branch, last one 3 years ago
broadinstitute
viral-ngs broadinstitute
67
191
other
30
Viral genomics analysis pipelines
bam fastq viral genome genomics illumina viral-ngs genome-assembly variant-calling genome-sequencing variant-annotations
Created 2014-09-25
3,233 commits to master branch, last one 3 months ago
aquaskyline
Clairvoyante aquaskyline
27
171
bsd-3-clause
16
Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing
deep-learning bioinformatics variant-calling computational-biology
Created 2017-07-21
276 commits to rbDev branch, last one 4 years ago
Illumina
paragraph Illumina
28
157
other
19
Graph realignment tools for structural variants
vcf htslib genotyping variant-calling structural-variation
Created 2017-11-24
33 commits to master branch, last one 2 years ago
sequana
sequana sequana
27
145
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
6,389 commits to main branch, last one 2 months ago
broadinstitute
long-read-pipelines broadinstitute
24
142
bsd-3-clause
16
Long read production pipelines
wdl pipelines long-reads variant-calling de-novo-assembly
Created 2019-05-14
557 commits to main branch, last one 15 days ago
tseemann
nullarbor tseemann
37
136
gpl-2.0
21
:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology
fastq report bacteria virulome resistome genotyping phylogenomics public-health denovo-assembly variant-calling
Created 2015-01-08
354 commits to master branch, last one 4 years ago
CRG-CNAG
CalliNGS-NF CRG-CNAG
55
132
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 3 years ago
ShujiaHuang
ilus ShujiaHuang
35
130
gpl-3.0
5
A lightweight and handy variant calling pipeline generator for whole-genome sequencing (WGS) and whole exom sequencing data (WES) analysis. 一个简易且全面的 WGS/WES 分析流程生成器.
pipeline bioinformatics variant-calling workflow-management bioinformatics-pipeline whole-genome-sequencing
Created 2020-04-08
363 commits to master branch, last one 4 days ago
nf-core
viralrecon nf-core
114
128
mit
107
Assembly and intrahost/low-frequency variant calling for viral samples
ont artic viral virus covid19 nf-core amplicon assembly covid-19 illumina nanopore nextflow pipeline workflow sars-cov-2 metagenomics oxford-nanopore variant-calling long-read-sequencing
Created 2020-03-30
2,788 commits to master branch, last one about a year ago
PacificBiosciences
ccs PacificBiosciences
30
117
bsd-3-clause-clear
23
CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)
ccs pacbio consensus bioinformatics variant-calling machine-learning
Created 2016-07-13
1,564 commits to develop branch, last one 9 months ago
humanlongevity
HLA humanlongevity
52
106
other
10
xHLA: Fast and accurate HLA typing from short read sequence data
genomics variants hla-typing sequencing variant-calling
Created 2017-06-20
160 commits to master branch, last one 7 years ago
HKU-BAL
Clair HKU-BAL
12
104
bsd-3-clause
6
Clair: Exploring the limit of using deep neural network on pileup data for germline variant calling
deep-learning bioinformatics variant-calling computational-biology
Created 2019-03-11
549 commits to master branch, last one 3 years ago
gear-genomics
tracy gear-genomics
21
101
bsd-3-clause
7
Basecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files
pcr indel tracy alignment sequencing crispr-cas9 chromatogram pcr-products crispr-analysis indel-discovery variant-calling sanger-sequencing genetic-engineering sanger-chromatograms sanger-trace-alignment
Created 2018-06-14
375 commits to main branch, last one 2 months ago
kcleal
dysgu kcleal
12
100
mit
3
Toolkit for calling structural variants using short or long reads
variant genomics long-read paired-end structural bioinformatics variant-calling structural-variation
Created 2019-10-30
568 commits to master branch, last one about a month ago
GenomicsDB
GenomicsDB GenomicsDB
17
97
other
11
High performance data storage for importing, querying and transforming variants.
cpp mpi gatk java scala spark variant genomics genomicsdb bioinformatics variant-calling precision-medicine
Created 2018-08-03
1,965 commits to master branch, last one 19 days ago
moiexpositoalonsolab
grenepipe moiexpositoalonsolab
21
95
gpl-3.0
4
A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles.
snakemake ancient-dna variant-calls pool-sequencing variant-calling snakemake-workflow population-genetics evolve-and-resequence genomic-variant-calling
Created 2020-05-06
589 commits to master branch, last one 18 days ago
iqbal-lab-org
gramtools iqbal-lab-org
15
94
mit
8
Genome inference from a population reference graph
prg python embl-ebi c-plus-plus genome-graph bioinformatics reference-graph variant-calling
Created 2015-04-10
1,359 commits to main branch, last one 2 years ago
nf-core
raredisease nf-core
37
92
mit
158
Call and score variants from WGS/WES of rare disease patients.
snv wes wgs nf-core nextflow pipeline workflow diagnostics rare-disease variant-calling variant-annotation structural-variants
Created 2021-06-21
2,676 commits to master branch, last one 3 months ago
TileDB-Inc
TileDB-VCF TileDB-Inc
16
91
mit
16
Efficient variant-call data storage and retrieval library using the TileDB storage library.
vcf gwas spark python tiledb genomics data-science bioinformatics variant-calling
Created 2019-09-04
1,155 commits to main branch, last one 19 days ago
lh3
minipileup lh3
6
84
unknown
4
Simple pileup-based variant caller
bioinformatics variant-calling
Created 2024-03-31
15 commits to master branch, last one 9 months ago