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ngs

Here are 479 public repositories matching this topic...

google / deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

science machine-learning bioinformatics deep-learning genomics genome tensorflow ngs sequencing dna deep-neural-network deepvariant

Updated Jan 28, 2022
Python

OpenGene / fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

adapter quality bioinformatics quality-control filter ngs sequencing overlap splitting duplication umi trimming preprocessing filtering illumina fastq merging qc polyg

Updated Feb 3, 2022
C++

broadinstitute / gatk

Official code repository for GATK versions 4 and up

java science bioinformatics spark genomics genome cluster ngs sequencing gatk-jar dna gatk

Updated Feb 23, 2022
Java

galaxyproject / galaxy

Data intensive science for everyone.

docker science workflow bioinformatics pipeline genomics workflow-engine ngs sequencing dna usegalaxy hacktoberfest

Updated Feb 23, 2022
Python

samtools / htslib

C library for high-throughput sequencing data formats

bioinformatics ngs sam vcf bam htslib bcf cram

Updated Feb 23, 2022
C

deeptools / deepTools

Tools to process and analyze deep sequencing data.

python bioinformatics rna-seq genomics ngs chip-seq

Updated Feb 11, 2022
Python

jvarkit

lindenb / jvarkit

Java utilities for Bioinformatics

java science bioinformatics genomics wiki biology ngs java-utilities next-generation-sequencing

Updated Feb 17, 2022
Java

maxplanck-ie / snakepipes

Customizable workflows based on snakemake and python for the analysis of NGS data

workflow rna-seq snakemake ngs hi-c chip-seq atac-seq bisulfite-sequencing

Updated Feb 1, 2022
Python

aidenlab / juicer

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

bioinformatics genomics ngs hi-c 3d-genome 3d-genome-browser

Updated Feb 9, 2022
Shell

samtools / htsjdk

A Java API for high-throughput sequencing data (HTS) formats.

java genomics gradle intellij jar ngs sequencing oracle sam vcf dna java-api fasta bam failure cram htsjdk

Updated Feb 19, 2022
Java

training-material

galaxyproject / training-material

A collection of Galaxy-related training material

training tutorial materials ngs metagenomics rnaseq proteomics chip-seq usegalaxy hacktoberfest

Updated Feb 24, 2022
HTML

fulcrumgenomics / fgbio

Sponsor

Tools for working with genomic and high throughput sequencing data.

bioinformatics scala ngs umi analyzing-genomic-data fgbio molecular-indexes

Updated Feb 23, 2022
Scala

OpenGene / AfterQC

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

bioinformatics quality-control ngs sequencing overlap error trimming filtering fastq qc adapter-trimming

Updated May 14, 2020
Python

hms-dbmi / scde

R package for analyzing single-cell RNA-seq data

bioinformatics r analysis ngs transcriptomics single-cell heterogenity

Updated Apr 5, 2020
R

ugene

ugeneunipro / ugene

UGENE is free open-source cross-platform bioinformatics software

science workflow bioinformatics cross-platform pipeline cpp ngs sequencing qt5 dna msa ugene

Updated Feb 24, 2022
C++

bioconvert / bioconvert

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

Updated Apr 17, 2020
Python

ngless-toolkit / ngless

Open

Add ability to strip sequences/qualities from SAM/BAM files

7

unode commented Feb 28, 2019

When working with very large SAM files it is often convenient to remove sequence and quality information to reduce storage and improve I/O.

Following from this it would be convenient to have a stripSeqQual function that replaces the two fields with *.

Read more

good first issue help wanted

Open

Implement API to cleanup unnecessary files

OpenGene / MutScan

Detect and visualize target mutations by scanning FastQ files directly

visualization bioinformatics validation cancer detection ngs mutation variant fastq somatic

Updated Feb 10, 2022
C

lucapinello / CRISPResso

Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data

python docker ngs crispr-analysis crispr amplicon crispr-cas9 cas9

Updated May 17, 2019
Python

sequana / sequana

Sequana: a set of Snakemake NGS pipelines

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

Updated Feb 21, 2022
Jupyter Notebook

jdidion / atropos

An NGS read trimming tool that is specific, sensitive, and speedy. (production)

bioinformatics ngs python3 trimming

Updated Jul 29, 2021
Python

zhanxw / rvtests

Rare variant test software for next generation sequencing data

c-plus-plus gwas kernel genetics ngs next-generation-sequencing variants meta-analysis genotype umich skat association-analysis rare-variant vcf-files

Updated Jan 26, 2022
C++

epam / cloud-pipeline

Cloud agnostic genomics analysis, scientific computation and storage platform

aws cloud chemistry azure biology ngs google-cloud modelling

Updated Feb 24, 2022
Java

cLoops

YaqiangCao / cLoops

Accurate and flexible loops calling tool for 3D genomic data.

Updated Feb 1, 2022
Python

lgmgeo / AnnotSV

Annotation and Ranking of Structural Variation

annotation genetics ngs ranking cnv sv priorization

Updated Jan 25, 2022
Tcl

ncbi / TPMCalculator

TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files

rna-seq ngs tpm

Updated Jan 19, 2021
C++

OpenGene / gencore

Generate duplex/single consensus reads to reduce sequencing noises and remove duplications

bioinformatics duplex ngs sequencing consensus duplication deduplication somatic deep-sequencing sequencing-error sequencing-noise duplex-sequencing

Updated Oct 29, 2021
C++

OpenGene / fastv

An ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. This tool can be used to detect viral infectious diseases, like COVID-19.

visualization bioinformatics virus ngs sequencing viral 2019-ncov coronavirus covid-19 covid sars-cov-2 hcov mngs viral-infectious-diseases microbial-sequences meta-genomics

Updated Sep 29, 2020
C++

seq2science

vanheeringen-lab / seq2science

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.

bioinformatics rna-seq snakemake pipeline reproducible-research ngs bioinformatics-pipeline chip-seq atac-seq workflows fastq sra

Updated Feb 23, 2022
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

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