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ngs

Here are 504 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 Mar 7, 2022
Python

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 Apr 29, 2022
Java

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 Mar 23, 2022
C++

galaxyproject / galaxy

Data intensive science for everyone.

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

Updated Apr 29, 2022
Python

samtools / htslib

C library for high-throughput sequencing data formats

bioinformatics ngs sam vcf bam htslib bcf cram

Updated Apr 29, 2022
C

deeptools / deepTools

Tools to process and analyze deep sequencing data.

python bioinformatics rna-seq genomics ngs chip-seq

Updated Mar 1, 2022
Python

jvarkit

lindenb / jvarkit

Java utilities for Bioinformatics

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

Updated Apr 29, 2022
Java

flowhub-team / awesome-omics

A collection of awesome things regarding all omics.

awesome genomics ngs protein omics single-cell ngs-pipeline wgs-analysis

Updated Mar 22, 2022

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 Apr 29, 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 Apr 29, 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 Apr 27, 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 Apr 29, 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 Apr 29, 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 Apr 29, 2022
C++

bioconvert / bioconvert

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

bioinformatics conversion ngs sniffer sequence convertor phylogeny bam2sam sam2bam bam2cram bcf2vcf bigbed2bed cram2bam cram2sam embl2ena embl2fasta embl2genbank fasta2fastq genbank2embl genbank2fasta

Updated Apr 15, 2022
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 Apr 20, 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 Apr 29, 2022
Java

cLoops

YaqiangCao / cLoops

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

python bioinformatics algorithm pipeline tool clustering ngs sequencing example-data hi-c dbscan 3d-genome chia-pet chromatin-interaction stripes hichip chromatin-loops chromatin-stripes loops-calling trac-looping

Updated Feb 1, 2022
Python

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 Apr 29, 2022
Python

ncbi / TPMCalculator

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

rna-seq ngs tpm

Updated Jan 19, 2021
C++

lgmgeo / AnnotSV

Annotation and Ranking of Structural Variation

annotation genetics ngs ranking cnv sv priorization

Updated Jan 25, 2022
Tcl

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++

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