next-generation-sequencing
There are 241 repositories under next-generation-sequencing topic.
ablab/spades
SPAdes Genome Assembler
lindenb/jvarkit
Java utilities for Bioinformatics
nf-core/sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
openbiox/awosome-bioinformatics
A curated list of resources for learning bioinformatics.
sanger-pathogens/Roary
Rapid large-scale prokaryote pan genome analysis
philres/ngmlr
NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations
bioinformatics-centre/kaiju
Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
sanger-pathogens/snp-sites
Finds SNP sites from a multi-FASTA alignment file
sanger-pathogens/Artemis
Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation
sanger-pathogens/circlator
A tool to circularize genome assemblies
nextstrain/nextclade
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
nickjcroucher/gubbins
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
sanger-pathogens/ariba
Antimicrobial Resistance Identification By Assembly
ngless-toolkit/ngless
NGLess: NGS with less work
zhanxw/rvtests
Rare variant test software for next generation sequencing data
alastair-droop/fqtools
An efficient FASTQ manipulation suite
SciLifeLab/Sarek
Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing
sanger-pathogens/assembly-stats
Get assembly statistics from FASTA and FASTQ files
chasewnelson/SNPGenie
Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
xjtu-omics/msisensor-pro
Microsatellite Instability (MSI) detection using high-throughput sequencing data.
Griffan/VerifyBamID
VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.
MicrobeLab/DeepMicrobes
DeepMicrobes: taxonomic classification for metagenomics with deep learning
Cibiv/NextGenMap
NextGenMap is a flexible highly sensitive short read mapping tool that handles much higher mismatch rates than comparable algorithms while still outperforming them in terms of runtime. This allows analysing large scale datasets even with increased SNP rates or higher error rates (e.g. caused by specialized experimental protocols) and avoids biases caused by highly variable regions in the genome.
chanzuckerberg/czid-web
Infectious Disease Sequencing Platform
KHP-Informatics/ngseasy
Dockerised Next Generation Sequencing Pipeline (QC, Align, Calling, Annotation)
stjude-rust-labs/fq
Command line utility for manipulating Illumina-generated FASTQ files.
tobiasrausch/ATACseq
Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
sanger-pathogens/Fastaq
Python3 scripts to manipulate FASTA and FASTQ files
sanger-pathogens/assembly_improvement
Improve the quality of a denovo assembly by scaffolding and gap filling
sanger-pathogens/iva
de novo virus assembler of Illumina paired reads
s4hts/HTStream
A high throughput sequence read toolset using a streaming approach facilitated by Linux pipes
epigen/MrBiomics
MrBiomics: Modules & Recipes augment Bioinformatics for Multi-Omics Analyses
YaqiangCao/cLoops2
Enhanced and elegant flexible peak/loop/domain -calling and analysis tool for 1D/3D genomic data.
stjude-rust-labs/wdl
Rust crates for working with Workflow Description Language (WDL) documents.
KHP-Informatics/DNAscan
DNAscan is a fast and efficient bioinformatics pipeline that allows for the analysis of DNA Next Generation sequencing data, requiring very little computational effort and memory usage.