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variant-calling

Here are 184 public repositories matching this topic...

tanghaibao / jcvi

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

bioinformatics genomics assembly blast comparative-genomics variant-calling synteny sequence-alignments genome-sequencing genetic-maps allmaps

Updated Apr 22, 2022
Python

vcflib / vcflib

C++ library and cmdline tools for parsing and manipulating VCF files

genomics variant-calling genotyping haplotypecaller vcf-manipulation

Updated May 2, 2022
C++

tseemann / snippy

✂️

⚡ Rapid haploid variant calling and core genome alignment

snps vcf variant-calling bacteria indel-discovery haploid fastq-analysis

Updated Sep 7, 2021
Perl

luntergroup / octopus

Bayesian haplotype-based mutation calling

bioinformatics genomics somatic-variants haplotypes variants variant-calling single-cell phasing de-novo-mutation

Updated Apr 26, 2022
C++

atks / vt

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

variant-calling

Updated May 4, 2021
C

broadinstitute / viral-ngs

Viral genomics analysis pipelines

genomics genome variant-calling bam genome-sequencing illumina fastq genome-assembly variant-annotations viral-ngs viral

Updated Nov 3, 2020
Python

nf-core / sarek

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

workflow bioinformatics pipeline annotation genomics nextflow cancer reproducible-research containers conda next-generation-sequencing variant-calling somatic germline whole-exome-sequencing whole-genome-sequencing pre-processing nf-core gatk4 target-panels

Updated May 3, 2022
Nextflow

aquaskyline / Clairvoyante

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

bioinformatics deep-learning computational-biology variant-calling

Updated Nov 4, 2020
Python

kishwarshafin / pepper

PEPPER-Margin-DeepVariant

nanopore variants variant-calling oxford-nanopore genome-variation long-reads pacbio-ccs assembly-polishing

Updated Mar 17, 2022
Python

nanoporetech / megalodon

Open

Updating "file formats" docs for additional clarity?

2

lyijin commented Oct 28, 2021

Hi there,

Thanks for writing such an excellent piece of software. The pace of development has definitely outstripped the updates in documentation--and as a newbie to ONT analysis, I was hoping that I could point out some of the pain points and help improve docs for others in my shoes.

The doc that I depended the most on was https://nanoporetech.github.io/megalodon/file_formats.html.

**Lin

Read more

documentation good first issue

suhrig / arriba

Fast and accurate gene fusion detection from RNA-Seq data

rna-seq cancer gene-fusion star variant-calling virus-integration structural-variation fusion-genes gene-fusions fusion-gene

Updated Apr 8, 2022
C++

sequana / sequana

Sequana: a set of Snakemake NGS pipelines

coverage rna-seq snakemake taxonomy ngs pacbio variant-calling de-novo sequanix

Updated Apr 20, 2022
Jupyter Notebook

Illumina / paragraph

Graph realignment tools for structural variants

vcf variant-calling htslib structural-variation genotyping

Updated Mar 9, 2022
C++

mcveanlab / mccortex

De novo genome assembly and multisample variant calling

genomics variant-calling kmer cortex genome-analysis genome-assembly de-bruijn-graphs genome-graph contigs

Updated Mar 28, 2019
C

lh3 / fermikit

De novo assembly based variant calling pipeline for Illumina short reads

bioinformatics genomics variant-calling denovo-assembly

Updated Nov 30, 2020
TeX

tseemann / nullarbor

💾

📃 "Reads to report" for public health and clinical microbiology

public-health report variant-calling bacteria fastq phylogenomics denovo-assembly genotyping resistome virulome

Updated Aug 3, 2020
Perl

HKU-BAL / Clair3

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

deep-learning nanopore genomics computational-biology variant-calling long-reads ont-data ont-models

Updated May 3, 2022
Python

HKU-BAL / Clair

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

bioinformatics deep-learning computational-biology variant-calling

Updated May 17, 2021
Python

CRG-CNAG / CalliNGS-NF

GATK RNA-Seq Variant Calling in Nextflow

bioinformatics rna-seq genomics nextflow ngs gatk variant-calling

Updated Aug 25, 2021
Nextflow

ccs

PacificBiosciences / ccs

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

machine-learning bioinformatics consensus pacbio variant-calling ccs

Updated Apr 19, 2022

iqbal-lab-org / gramtools

Genome inference from a population reference graph

python c-plus-plus bioinformatics variant-calling genome-graph embl-ebi prg reference-graph

Updated Mar 16, 2022
C++

humanlongevity / HLA

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

genomics sequencing variants variant-calling hla-typing

Updated Oct 11, 2018
Jupyter Notebook

bioinformatics-centre / BayesTyper

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

ngs bayesian-inference variant-calling indels gibbs-sampling structural-variation snvs dna-sequencing genotyping k-mers variant-graphs

Updated Apr 1, 2019
C++

ivar

andersen-lab / ivar

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

variant-calling amplicon-sequencing

Updated Apr 23, 2022
C++

gear-genomics / tracy

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

sequencing alignment crispr-analysis variant-calling pcr tracy crispr-cas9 sanger-chromatograms indel-discovery chromatogram sanger-trace-alignment sanger-sequencing pcr-products genetic-engineering indel

Updated Apr 30, 2022
C++

nf-core / viralrecon

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

workflow nanopore virus pipeline nextflow assembly metagenomics variant-calling illumina oxford-nanopore amplicon viral ont nf-core long-read-sequencing artic covid-19 covid19 sars-cov-2

Updated Apr 26, 2022
Nextflow

GenomicsDB / GenomicsDB

Highly performant data storage in C++ for importing, querying and transforming variant data with C/C++/Java/Spark bindings. Used in gatk4.

java scala spark genomics cpp mpi variant-calling variant genomics-data genomicsdb

Updated May 3, 2022
C++

broadinstitute / long-read-pipelines

Open

Optimize Nanoplot step

1

SHuang-Broad commented Dec 11, 2021

Currently, the task NanoPlotFromBam takes over 4 hours frequently, easily the longest (wall-clock) running task, with 16 threads and 32 G memory.

Makes sense to investigate why it takes so long.

Read more

good first issue optimization tool-specific

Open

Update workflows' output with finish date

1

Open

Unify procedure scatter-gather for small variant calling

Find more good first issues

ShujiaHuang / ilus

A handy variant calling pipeline generator for whole genome re-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.

bioinformatics ngs vcf bioinformatics-pipeline variant-calling whole-genome-sequencing

Updated Apr 27, 2022
Python

czbiohub / cerebra

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

genomics mutations scrna-seq variant-calling

Updated Sep 9, 2021
Python

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