tanghaibao/jcvi

Python library to facilitate genome assembly, annotation, and comparative genomics

Language: Python - Size: 17.8 MB - Last synced: 4 days ago - Pushed: 6 days ago - Stars: 701 - Forks: 180

vcflib/vcflib

C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings

Language: C++ - Size: 32.9 MB - Last synced: about 21 hours ago - Pushed: 22 days ago - Stars: 604 - Forks: 219

tseemann/snippy

:scissors: :zap: Rapid haploid variant calling and core genome alignment

Language: Perl - Size: 124 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 408 - Forks: 111

nf-core/sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

Language: Nextflow - Size: 82.4 MB - Last synced: 27 days ago - Pushed: 27 days ago - Stars: 333 - Forks: 370

luntergroup/octopus

Bayesian haplotype-based mutation calling

Language: C++ - Size: 137 MB - Last synced: 11 days ago - Pushed: 9 months ago - Stars: 296 - Forks: 37

kishwarshafin/pepper

PEPPER-Margin-DeepVariant

Language: Python - Size: 36.1 MB - Last synced: 16 days ago - Pushed: 4 months ago - Stars: 231 - Forks: 41

HKU-BAL/Clair3

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

Language: Python - Size: 3.11 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 220 - Forks: 26

suhrig/arriba

Fast and accurate gene fusion detection from RNA-Seq data

Language: C++ - Size: 24.1 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 206 - Forks: 49

atks/vt

A tool set for short variant discovery in genetic sequence data.

Language: C - Size: 30.1 MB - Last synced: 7 months ago - Pushed: about 3 years ago - Stars: 190 - Forks: 3

nanoporetech/megalodon

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 to a reference genome/transriptome.

Language: Python - Size: 24.9 MB - Last synced: 6 days ago - Pushed: about 1 year ago - Stars: 190 - Forks: 29

broadinstitute/viral-ngs

Viral genomics analysis pipelines

Language: Python - Size: 64.5 MB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 180 - Forks: 66

aquaskyline/Clairvoyante

Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing

Language: Python - Size: 894 MB - Last synced: 11 days ago - Pushed: 5 months ago - Stars: 172 - Forks: 27

Illumina/paragraph

Graph realignment tools for structural variants

Language: C++ - Size: 30.8 MB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 143 - Forks: 28

sequana/sequana

Sequana: a set of Snakemake NGS pipelines

Language: Jupyter Notebook - Size: 35.5 MB - Last synced: about 2 hours ago - Pushed: 2 months ago - Stars: 141 - Forks: 27

CRG-CNAG/CalliNGS-NF

GATK RNA-Seq Variant Calling in Nextflow

Language: Nextflow - Size: 29 MB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 129 - Forks: 52

tseemann/nullarbor

:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology

Language: Perl - Size: 11.3 MB - Last synced: 7 months ago - Pushed: almost 4 years ago - Stars: 123 - Forks: 35

andersen-lab/ivar Fork of gkarthik/ivar

iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.

Language: C++ - Size: 16 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 115 - Forks: 38

broadinstitute/long-read-pipelines

Long read production pipelines

Language: Jupyter Notebook - Size: 179 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 111 - Forks: 22

nf-core/viralrecon

Assembly and intrahost/low-frequency variant calling for viral samples

Language: Nextflow - Size: 9.67 MB - Last synced: 9 days ago - Pushed: 10 days ago - Stars: 108 - Forks: 97

lh3/fermikit

De novo assembly based variant calling pipeline for Illumina short reads

Language: TeX - Size: 7.45 MB - Last synced: 11 days ago - Pushed: over 3 years ago - Stars: 108 - Forks: 23

mcveanlab/mccortex

De novo genome assembly and multisample variant calling

Language: C - Size: 9.86 MB - Last synced: 7 months ago - Pushed: about 5 years ago - Stars: 107 - Forks: 24

ShujiaHuang/ilus

A 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.

Language: Python - Size: 780 KB - Last synced: 17 days ago - Pushed: 4 months ago - Stars: 107 - Forks: 35

PacificBiosciences/ccs

CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)

Size: 34.1 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 105 - Forks: 31

HKU-BAL/Clair

Clair: Exploring the limit of using deep neural network on pileup data for germline variant calling

Language: Python - Size: 1.01 MB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 102 - Forks: 12

gear-genomics/tracy

Basecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files

Language: C++ - Size: 3.17 MB - Last synced: about 1 month ago - Pushed: about 2 months ago - Stars: 94 - Forks: 19

humanlongevity/HLA

xHLA: Fast and accurate HLA typing from short read sequence data

Language: Jupyter Notebook - Size: 91.3 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 92 - Forks: 51

GenomicsDB/GenomicsDB

High performance data storage for importing, querying and transforming variants.

Language: C++ - Size: 65.9 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 89 - Forks: 18

iqbal-lab-org/gramtools

Genome inference from a population reference graph

Language: C++ - Size: 14.7 MB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 89 - Forks: 14

kcleal/dysgu

Toolkit for calling structural variants using short or long reads

Language: Cython - Size: 46.3 MB - Last synced: 23 days ago - Pushed: 23 days ago - Stars: 85 - Forks: 10

bioinformatics-centre/BayesTyper

A method for variant graph genotyping based on exact alignment of k-mers

Language: C++ - Size: 1.75 MB - Last synced: 5 months ago - Pushed: about 5 years ago - Stars: 83 - Forks: 8

TileDB-Inc/TileDB-VCF

Efficient variant-call data storage and retrieval library using the TileDB storage library.

Language: C++ - Size: 33 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 79 - Forks: 13

moiexpositoalonsolab/grenepipe

A flexible, scalable, and reproducible pipeline to automate variant calling from sequence reads.

Language: Python - Size: 93.2 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 78 - Forks: 18

lh3/minipileup

Simple pileup-based variant caller

Language: C - Size: 93.8 KB - Last synced: 11 days ago - Pushed: about 2 months ago - Stars: 76 - Forks: 3

nf-core/raredisease

Call and score variants from WGS/WES of rare disease patients.

Language: Nextflow - Size: 11.2 MB - Last synced: about 7 hours ago - Pushed: about 8 hours ago - Stars: 72 - Forks: 34

TimD1/vcfdist

vcfdist: Accurately benchmarking phased variant calls

Language: C++ - Size: 61.4 MB - Last synced: 11 days ago - Pushed: 11 days ago - Stars: 67 - Forks: 5

czbiohub-sf/cerebra 📦

A tool for fast and accurate summarizing of variant calling format (VCF) files

Language: Python - Size: 164 MB - Last synced: 2 days ago - Pushed: over 1 year ago - Stars: 59 - Forks: 9

lh3/CHM-eval

Language: TeX - Size: 524 KB - Last synced: 11 days ago - Pushed: almost 4 years ago - Stars: 49 - Forks: 8

karel-brinda/ococo

Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.

Language: C++ - Size: 3.49 MB - Last synced: 7 months ago - Pushed: over 5 years ago - Stars: 47 - Forks: 4

Clinical-Genomics/BALSAMIC

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

Language: Python - Size: 228 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 43 - Forks: 16

NVIDIA-Genomics-Research/VariantWorks

Deep Learning based variant calling toolkit - https://clara-parabricks.github.io/VariantWorks/

Language: Python - Size: 10.1 MB - Last synced: 15 days ago - Pushed: over 1 year ago - Stars: 43 - Forks: 11

gencorefacility/variant-calling-pipeline-gatk4

Variant Calling Pipeline Using GATK4 and Nextflow

Language: Nextflow - Size: 23.4 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 40 - Forks: 40

kevlar-dev/kevlar

Reference-free variant discovery in large eukaryotic genomes

Language: Python - Size: 71.5 MB - Last synced: about 1 month ago - Pushed: almost 3 years ago - Stars: 40 - Forks: 9

nf-core/deepvariant Fork of lifebit-ai/DeepVariant 📦

Please consider using/contributing to https://github.com/nf-core/sarek

Language: Nextflow - Size: 7.18 MB - Last synced: 5 months ago - Pushed: almost 3 years ago - Stars: 40 - Forks: 18

brentp/indelope

find large indels (in the blind spot between GATK/freebayes and SV callers)

Language: Nim - Size: 133 KB - Last synced: 18 days ago - Pushed: over 6 years ago - Stars: 39 - Forks: 1

kehrlab/PopDel

Population-wide Deletion Calling

Language: C++ - Size: 20.4 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 33 - Forks: 2

gear-genomics/indigo

Indigo: SNV and InDel Discovery in Chromatogram traces obtained from Sanger sequencing of PCR products

Language: JavaScript - Size: 2.72 MB - Last synced: about 1 month ago - Pushed: 7 months ago - Stars: 30 - Forks: 6

oliverSI/GATK4_Best_Practice

GATK4 Best Practice Nextflow Pipeline

Size: 9.77 KB - Last synced: 8 months ago - Pushed: over 6 years ago - Stars: 29 - Forks: 28

HKU-BAL/ClairS-TO

ClairS-TO - a deep-learning method for tumor-only somatic variant calling

Language: Python - Size: 1.93 MB - Last synced: 23 days ago - Pushed: 24 days ago - Stars: 29 - Forks: 2

nf-core/rnavar

gatk4 RNA variant calling pipeline

Language: Nextflow - Size: 3.64 MB - Last synced: 10 days ago - Pushed: 10 days ago - Stars: 28 - Forks: 29

sib-swiss/NGS-variants-training

GitHub for the SIB courses NGS - Genome variant analysis

Language: Shell - Size: 68.1 MB - Last synced: about 1 month ago - Pushed: 3 months ago - Stars: 24 - Forks: 9

aryarm/varCA

Use an ensemble of variant callers to call variants from ATAC-seq data

Language: Python - Size: 354 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 21 - Forks: 7

SUwonglab/arcsv

Complex structural variant detection from WGS data

Language: Python - Size: 5.1 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 20 - Forks: 6

IKIM-Essen/uncovar

Transparent and robust SARS-CoV-2 variant calling and lineage assignment with comprehensive reporting.

Language: Python - Size: 3.83 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 20 - Forks: 4

Sentieon/sentieon-dnaseq 📦

Sentieon DNAseq

Language: Shell - Size: 60.5 KB - Last synced: 5 months ago - Pushed: over 3 years ago - Stars: 19 - Forks: 12

sanjaynagi/rna-seq-pop

Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data

Language: Jupyter Notebook - Size: 99.6 MB - Last synced: 19 days ago - Pushed: 23 days ago - Stars: 17 - Forks: 6

adrianodemarino/Imputation_beagle_tutorial

Imputation-beagle-tutorial

Size: 12.7 KB - Last synced: 7 months ago - Pushed: almost 2 years ago - Stars: 16 - Forks: 2

tjiangHIT/rMETL

rMETL - realignment-based Mobile Element insertion detection Tool for Long read

Language: Python - Size: 1.02 MB - Last synced: 24 days ago - Pushed: 9 months ago - Stars: 15 - Forks: 3

nf-core/exoseq 📦

Please consider using/contributing to https://github.com/nf-core/sarek

Language: Nextflow - Size: 2.77 MB - Last synced: 5 months ago - Pushed: over 5 years ago - Stars: 14 - Forks: 25

nf-core/vipr 📦

Assembly and intrahost / low-frequency variant calling for viral samples

Language: Nextflow - Size: 217 KB - Last synced: 4 months ago - Pushed: over 4 years ago - Stars: 14 - Forks: 10

NBISweden/workshop-ngsintro

Workshop • Intro to Bioinformatics using NGS data • 5 days

Language: HTML - Size: 695 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 12 - Forks: 5

TimD1/nPoRe

nPoRe: n-Polymer Realigner for improved pileup-based variant calling

Language: Python - Size: 493 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 12 - Forks: 0

HKU-BAL/Clair3-Trio

Clair3-Trio: variant calling in trio using Nanopore long-reads

Language: Python - Size: 2.74 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 12 - Forks: 1

collaborativebioinformatics/Sniphles

Sniphles is a read-based phasing approach for phased variant calling of structural variants.

Language: Python - Size: 2.44 MB - Last synced: about 1 month ago - Pushed: over 3 years ago - Stars: 12 - Forks: 2

koesterlab/microphaser

Language: Rust - Size: 1.91 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 11 - Forks: 2

CMU-SAFARI/Genome-on-Diet

Genome-on-Diet is a fast and memory-frugal framework for exemplifying sparsified genomics for read mapping, containment search, and metagenomic profiling. It is much faster & more memory-efficient than minimap2 for Illumina, HiFi, and ONT reads. Described by Alser et al. (preliminary version: https://arxiv.org/abs/2211.08157).

Language: Roff - Size: 63 MB - Last synced: 23 days ago - Pushed: 8 months ago - Stars: 11 - Forks: 4

tobiasrausch/nRex

nRex: Germline and somatic single-nucleotide, short indel and structural variant calling

Language: Shell - Size: 1.85 MB - Last synced: 19 days ago - Pushed: 20 days ago - Stars: 11 - Forks: 1

mbhall88/tbpore

Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data

Language: Python - Size: 3.3 MB - Last synced: 17 days ago - Pushed: 7 months ago - Stars: 11 - Forks: 2

KChen-lab/MonoVar

Single nucleotide variant (SNV) detection and genotyping algorithm for single-cell DNA sequencing data

Language: Python - Size: 13.5 MB - Last synced: 7 months ago - Pushed: about 4 years ago - Stars: 11 - Forks: 6

Sydney-Informatics-Hub/Bioinformatics

A suite of bioinformatics data processing and analysis pipelines, software, and training resources for common DNA and RNA sequence analysis methods.

Size: 137 KB - Last synced: about 1 month ago - Pushed: about 2 months ago - Stars: 11 - Forks: 0

abs-tudelft/variant-calling-at-scale

Scalable and High Performance Variant Calling on Cluster Environments

Language: Python - Size: 818 KB - Last synced: 10 months ago - Pushed: over 2 years ago - Stars: 10 - Forks: 0

yjx1217/Varathon

A scalable variant calling and benchmarking framework supporting both short and long reads.

Language: Perl - Size: 934 KB - Last synced: 12 months ago - Pushed: over 3 years ago - Stars: 10 - Forks: 3

BioJulia/SequenceVariation.jl

Biological sequence variation

Language: Julia - Size: 371 KB - Last synced: about 1 month ago - Pushed: about 1 year ago - Stars: 9 - Forks: 3

pdimens/harpy

Process raw haplotagging data, from raw sequences to phased haplotypes, batteries included.

Language: Python - Size: 386 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 9 - Forks: 1

Sentieon/sentieon-dnascope-ml

Sentieon DNAscope + Machine Learning Model

Language: Shell - Size: 111 KB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 9 - Forks: 3

bgm-cwg/novoCaller

Language: C++ - Size: 62.5 KB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 8 - Forks: 1

dmnfarrell/snipgenie

command line and desktop tool for microbial variant calling

Language: Jupyter Notebook - Size: 122 MB - Last synced: 18 days ago - Pushed: about 1 month ago - Stars: 8 - Forks: 0

pblaney/mgp1000

Nextflow bioinformatics pipeline for large-scale analysis of Multiple Myeloma genomes

Language: Nextflow - Size: 324 MB - Last synced: 11 days ago - Pushed: 11 days ago - Stars: 8 - Forks: 4

VCCRI/dv-trio

dv-trio provides a pipeline to call variants for a trio (father-mother-child) using DeepVariants [1]. Genomic Variant Calling Files (gVCFs) created by DeepVariants are then co_called together using GATK[2]. The resultant trio VCF is then post-processing with FamSeq[3] to eliminate mendelian errors.

Language: Shell - Size: 165 KB - Last synced: about 2 months ago - Pushed: over 3 years ago - Stars: 8 - Forks: 1

CMU-SAFARI/Molecules2Variations

The first work to provide a comprehensive survey of a prominent set of algorithmic improvement and hardware acceleration efforts for the entire genome analysis pipeline used for the three most prominent sequencing data, short reads (Illumina), ultra-long reads (ONT), and accurate long reads (HiFi). Described in arXiv (2022) by Alser et al. https://arxiv.org/abs/2205.07957

Size: 4.31 MB - Last synced: 23 days ago - Pushed: almost 2 years ago - Stars: 8 - Forks: 0

tkonopka/GeneticThesaurus

Thesaurus for genetic variants

Language: Java - Size: 1.2 MB - Last synced: 3 months ago - Pushed: about 6 years ago - Stars: 8 - Forks: 1

kaist-ina/RUN-DVC

Generalizing deep learning-based variant callers via domain adaptation and semi-supervised learning

Language: Python - Size: 3.5 MB - Last synced: about 1 month ago - Pushed: 4 months ago - Stars: 8 - Forks: 0

INMEGEN/Pipelines_INMEGEN

Flujos de trabajos desarrollados y automatizados en el INMEGEN para el procesamiento de datos genómicos y transcriptómicos.

Language: Nextflow - Size: 3.06 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 7 - Forks: 0

fedarko/strainFlye

Pipeline for analyzing (rare) mutations in metagenome-assembled genomes

Language: Python - Size: 14.4 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 7 - Forks: 1

DKFZ-ODCF/SNVCallingWorkflow

The DKFZ-ODCF, formerly DKFZ/eilslabs SNV-Calling Workflow

Language: Python - Size: 925 KB - Last synced: 7 months ago - Pushed: 11 months ago - Stars: 7 - Forks: 4

lindechun/VirVarDP

Virus variant detection pipeline

Language: Python - Size: 575 KB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 7 - Forks: 0

bioinf/RMAhunter

Language: HTML - Size: 116 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 7 - Forks: 0

HKU-BAL/Clair3-RNA

Clair3-RNA - a long-read small variant caller for RNA sequencing data

Language: Python - Size: 327 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 7 - Forks: 0

mcveanlab/Corticall

Germline DNM caller based on LdBG assembly of pathogens

Language: Java - Size: 128 MB - Last synced: 8 months ago - Pushed: about 4 years ago - Stars: 7 - Forks: 3

hitbc/rMETL Fork of tjiangHIT/rMETL

rMETL - realignment-based Mobile Element insertion detection Tool for Long read

Language: Python - Size: 1.04 MB - Last synced: 10 months ago - Pushed: over 4 years ago - Stars: 6 - Forks: 0

Cristianetaniguti/Reads2Map

WDL workflows to build genetic maps from sequencing reads

Language: WDL - Size: 167 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 6 - Forks: 0

ucladx/pancan-panel-design

A pan-cancer DNA-seq panel

Language: Python - Size: 3.31 MB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 6 - Forks: 0

tobiasrausch/covid19

SARS-CoV-2 analysis pipeline for short-read, paired-end illumina sequencing

Language: Python - Size: 324 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 6 - Forks: 1

elowy01/vcf_filtering

Filter a VCF to discard false positive variants

Language: Python - Size: 72.3 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 6 - Forks: 0

aprilweilab/picovcf

Single-header C++ library for fast/low-memory VCF (Variant Call Format) parsing.

Language: C++ - Size: 151 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 6 - Forks: 0

brwnj/freebayes-nf

a better freebayes-parallel

Language: Nextflow - Size: 21.5 KB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 6 - Forks: 1

CRG-CNAG/ngs2017ws-docs

NGS 2017 Post-Conference Workshop Documentation

Language: CSS - Size: 13 MB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 5 - Forks: 1

allytrope/variant-analysis

A Snakemake pipeline for variant calling of genomic FASTQ data using GATK

Language: Python - Size: 2.1 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 5 - Forks: 0

NCI-CGR/GEMSCAN

Joint variant calling with GATK4 HaplotypeCaller, Google DeepVariant 1.0.0 and Strelka2, coordinated via Snakemake.

Language: Python - Size: 17.4 MB - Last synced: 18 days ago - Pushed: 18 days ago - Stars: 5 - Forks: 7

tobiasrausch/rdxon

Reference-free FASTQ filter for rare germline and somatic variants

Language: C++ - Size: 89.8 KB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 5 - Forks: 0

rice-systems/lofreq-fpga

FPGA Acceleration for the LoFreq variant caller

Language: C - Size: 20.5 KB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 5 - Forks: 0