Topic: ngs Goto Github

Some thing interesting about ngs

👇 Here are 607 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

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 bioinformatics genomics hi-c 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

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 plotting ngs ngs-analysis rna-seq igv

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

python3 bioinformatics ngs trimming

jodyphelan / tbprofiler

ngs,Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data

User: jodyphelan

drug-resistance mycobacterium tuberculosis ngs mycobacterium-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

splice-junctions indels dna rna realigner ngs abra

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,flexible suite of CLI tools for contact extraction (.pairs) from sequencing data (Hi-C, Micro-C and other chromosome capture methods)

Organization: open2c

3d-genome bioinformatics file-formatter hi-c ngs python pairs-file

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

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