Topic: ngs Goto Github

👇 Here are 623 public repositories matching this topic...

3dgenomes / tadbit
ngs,TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models
Organization: 3dgenomes
python chromatin mapping 3d-models hi-c ngs

ablab / isoquant
ngs,Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
Organization: ablab
Home Page: https://ablab.github.io/IsoQuant/
ngs transcriptomics pacbio nanopore bioinformatics rna-seq

aidenlab / juicer
ngs,A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
Organization: aidenlab
Home Page: http://aidenlab.org
3d-genome 3d-genome-browser genomics hi-c bioinformatics ngs

bioconvert / bioconvert
ngs,Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.
Organization: bioconvert
Home Page: http://bioconvert.readthedocs.io
ngs bam2sam conversion phylogeny sequence sam2bam bam2cram bcf2vcf bigbed2bed cram2bam

bioinformatics-centre / bayestyper
ngs,A method for variant graph genotyping based on exact alignment of k-mers
Organization: bioinformatics-centre
variant-calling genotyping ngs variant-graphs dna-sequencing snvs indels structural-variation bayesian-inference gibbs-sampling

broadinstitute / gatk
ngs,Official code repository for GATK versions 4 and up
Organization: broadinstitute
Home Page: https://software.broadinstitute.org/gatk
genomics spark science dna ngs sequencing genome bioinformatics gatk

cbg-ethz / v-pipe
ngs,V-pipe is a pipeline designed for analysing NGS data of short viral genomes
Organization: cbg-ethz
Home Page: https://cbg-ethz.github.io/V-pipe/
ngs snakemake conda biohackeu20 virus sequencing bioinformatics bioinformatics-pipeline biohackcovid20 sars-cov-2

costalab / reg-gen
ngs,Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
Organization: costalab
Home Page: https://reg-gen.readthedocs.io/
bioinformatics genomics differential-peak-calling footprinting ngs dnase-seq chip-seq atac-seq motif motif-analysis

crg-cnag / callings-nf
ngs,GATK RNA-Seq Variant Calling in Nextflow
Organization: crg-cnag
nextflow ngs variant-calling rna-seq gatk bioinformatics genomics

deeptools / deeptools
ngs,Tools to process and analyze deep sequencing data.
Organization: deeptools
python bioinformatics genomics ngs rna-seq chip-seq

epam / cloud-pipeline
ngs,Cloud agnostic genomics analysis, scientific computation and storage platform
Organization: epam
Home Page: https://cloud-pipeline.com
cloud aws azure ngs modelling biology chemistry google-cloud

flowhub-team / awesome-omics
ngs,A collection of awesome things regarding all omics.
User: flowhub-team
genomics protein single-cell ngs ngs-pipeline wgs-analysis awesome omics

fulcrumgenomics / fgbio
ngs,Tools for working with genomic and high throughput sequencing data.
Organization: fulcrumgenomics
Home Page: http://fulcrumgenomics.github.io/fgbio/
analyzing-genomic-data umi bioinformatics ngs scala fgbio molecular-indexes genomics

galaxyproject / galaxy
ngs,Data intensive science for everyone.
Organization: galaxyproject
Home Page: https://galaxyproject.org
bioinformatics workflow genomics science sequencing ngs dna usegalaxy pipeline workflow-engine hacktoberfest

galaxyproject / training-material
ngs,A collection of Galaxy-related training material
Organization: galaxyproject
Home Page: https://training.galaxyproject.org
usegalaxy training materials ngs tutorial metagenomics proteomics rnaseq chip-seq hacktoberfest

google / deepvariant
ngs,DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Organization: google
tensorflow deep-neural-network genomics science dna sequencing genome bioinformatics deep-learning ngs

harbourlab / spark
ngs,Publication quality NGS track plotting
User: harbourlab
bedgraph-files chip-seq igv ngs ngs-analysis plotting rna-seq

hms-dbmi / scde
ngs,R package for analyzing single-cell RNA-seq data
Organization: hms-dbmi
Home Page: http://pklab.med.harvard.edu/scde
bioinformatics single-cell transcriptomics heterogenity analysis r ngs

indexofire / pathongs
ngs,Pathogen NGS Documentary
User: indexofire
Home Page: https://indexofire.github.io/pathongs
pathogen ngs bioinformatics genomic-epidemiology hzcdc

jdidion / atropos
ngs,An NGS read trimming tool that is specific, sensitive, and speedy. (production)
User: jdidion
bioinformatics ngs python3 trimming

jodyphelan / tbprofiler
ngs,Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data
User: jodyphelan
drug-resistance mycobacterium mycobacterium-tuberculosis ngs tuberculosis

kaist-ina / bwa-meme
ngs,BWA-MEME: Faster BWA-MEM2 using learned-index
Organization: kaist-ina
Home Page: https://ina.kaist.ac.kr/projects/bwa-meme/
bioinformatics ngs alignment-algorithm bwa-mem bwa-mem2 genomics learned-index short-read-mapping machine-learning bwa-meme

khp-informatics / ngseasy
ngs,Dockerised Next Generation Sequencing Pipeline (QC, Align, Calling, Annotation)
Organization: khp-informatics
ngs docker next-generation-sequencing pipeline shell

khyox / recentrifuge
ngs,Recentrifuge: robust comparative analysis and contamination removal for metagenomics
User: khyox
Home Page: http://www.recentrifuge.org
metagenomics low-biomass centrifuge lmat clark kraken comparative-genomics ngs robustness contamination

lgmgeo / annotsv
ngs,Annotation and Ranking of Structural Variation
User: lgmgeo
genetics sv cnv annotation ranking priorization ngs

lindenb / jvarkit
ngs,Java utilities for Bioinformatics
User: lindenb
Home Page: https://jvarkit.readthedocs.io/
bioinformatics java next-generation-sequencing ngs science biology genomics

louiejtaylor / grabseqs
ngs,A utility for easy downloading of reads from next-gen sequencing repositories like NCBI SRA
User: louiejtaylor
bioinformatics metagenomics ngs sra ncbi-sra conda python

lucapinello / crispresso
ngs,Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data
User: lucapinello
crispr-analysis crispr-cas9 crispr cas9 ngs amplicon python docker

maxplanck-ie / snakepipes
ngs,Customizable workflows based on snakemake and python for the analysis of NGS data
Organization: maxplanck-ie
Home Page: http://snakepipes.readthedocs.io
ngs rna-seq chip-seq workflow atac-seq hi-c bisulfite-sequencing snakemake

mozack / abra2
ngs,ABRA2
User: mozack
abra dna indels ngs realigner rna splice-junctions

ncbi / tpmcalculator
ngs,TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files
Organization: ncbi
ngs rna-seq tpm

ngless-toolkit / ngless
ngs,NGLess: NGS with less work
Organization: ngless-toolkit
Home Page: https://ngless.embl.de
haskell bioinformatics bioinformatics-pipeline samtools bwa next-generation-sequencing fastq-format fastq science ngs

open2c / cooler
ngs,A cool place to store your Hi-C
Organization: open2c
Home Page: https://open2c.github.io/cooler
contact-matrix hdf5 python sparse genomics hi-c bioinformatics file-format cooler 3d-genome

open2c / pairtools
ngs,Extract 3D contacts (.pairs) from sequencing alignments
Organization: open2c
3d-genome bioinformatics file-formatter hi-c ngs pairs-file python

opengene / afterqc
ngs,Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
Organization: opengene
quality-control fastq ngs sequencing bioinformatics overlap trimming filtering error qc

opengene / fastp
ngs,An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
Organization: opengene
fastq qc preprocessing filtering adapter overlap quality trimming splitting quality-control filter ngs bioinformatics umi sequencing illumina polyg duplication merging

opengene / fastv
ngs,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.
Organization: opengene
covid-19 sars-cov-2 hcov 2019-ncov sequencing bioinformatics ngs mngs coronavirus covid

opengene / gencore
ngs,Generate duplex/single consensus reads to reduce sequencing noises and remove duplications
Organization: opengene
sequencing ngs bioinformatics sequencing-error consensus deep-sequencing sequencing-noise duplication duplex deduplication

opengene / mutscan
ngs,Detect and visualize target mutations by scanning FastQ files directly
Organization: opengene
mutation ngs bioinformatics visualization fastq variant detection cancer somatic validation

oschwengers / platon
ngs,Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.
User: oschwengers
Home Page: https://doi.org/10.1099/mgen.0.000398
microbiology bioinformatics plasmids ngs wgs contigs bacteria assembly

samtools / htsjdk
ngs,A Java API for high-throughput sequencing data (HTS) formats.
Organization: samtools
Home Page: http://samtools.github.io/htsjdk/
genomics sequencing dna ngs bam cram sam fasta vcf java-api

samtools / htslib
ngs,C library for high-throughput sequencing data formats
Organization: samtools
htslib bioinformatics sam bam cram vcf bcf ngs

seppinho / haplogrep-cmd
ngs,HaploGrep - mtDNA haplogroup classification. Supporting rCRS and RSRS.
User: seppinho
Home Page: https://haplogrep.i-med.ac.at/
mtdna haplogroup ngs snp-genotyping classificaton phylotree

sequana / sequana
ngs,Sequana: a set of Snakemake NGS pipelines
Organization: sequana
Home Page: http://sequana.readthedocs.io
ngs variant-calling taxonomy de-novo pacbio sequanix snakemake coverage rna-seq

sortmerna / sortmerna
ngs,SortMeRNA: next-generation sequence filtering and alignment tool
Organization: sortmerna
Home Page: https://sortmerna.readthedocs.io
cpp python alignment bioinformatics metatranscriptomics ngs sequencing

telatin / seqfu2
ngs,:rocket: seqfu - Sequece Fastx Utilities
User: telatin
Home Page: https://telatin.github.io/seqfu2
fastq fasta bioinformatics bioinformatics-tool bioconda genomics ngs sequencing

ugeneunipro / ugene
ngs,UGENE is free open-source cross-platform bioinformatics software
Organization: ugeneunipro
Home Page: http://ugene.net
ugene bioinformatics ngs dna workflow pipeline science cpp qt5 sequencing cross-platform msa

vanheeringen-lab / seq2science
ngs,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.
Organization: vanheeringen-lab
Home Page: https://vanheeringen-lab.github.io/seq2science
snakemake bioinformatics bioinformatics-pipeline atac-seq rna-seq chip-seq reproducible-research ngs pipeline sra

yaqiangcao / cloops
ngs,Accurate and flexible loops calling tool for 3D genomic data.
User: yaqiangcao
Home Page: https://yaqiangcao.github.io/cLoops/
3d-genome algorithm bioinformatics chia-pet chromatin-interaction chromatin-loops chromatin-stripes clustering dbscan example-data hi-c hichip loops-calling ngs pipeline python sequencing stripes tool trac-looping

zhanxw / rvtests
ngs,Rare variant test software for next generation sequencing data
User: zhanxw
next-generation-sequencing ngs association-analysis gwas rare-variant meta-analysis genotype skat c-plus-plus variants