next-generation-sequencing
There are 232 repositories under next-generation-sequencing topic.
ablab/spades
SPAdes Genome Assembler
lindenb/jvarkit
Java utilities for Bioinformatics
openbiox/awosome-bioinformatics
A curated list of resources for learning bioinformatics.
nf-core/sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
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
alastair-droop/fqtools
An efficient FASTQ manipulation suite
zhanxw/rvtests
Rare variant test software for next generation sequencing data
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.
KHP-Informatics/ngseasy
Dockerised Next Generation Sequencing Pipeline (QC, Align, Calling, Annotation)
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.
MicrobeLab/DeepMicrobes
DeepMicrobes: taxonomic classification for metagenomics with deep learning
chanzuckerberg/czid-web
Infectious Disease Sequencing Platform
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
YaqiangCao/cLoops2
Enhanced and elegant flexible peak/loop/domain -calling and analysis tool for 1D/3D genomic data.
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.
mehrdadbakhtiari/adVNTR
A tool for genotyping Variable Number Tandem Repeats (VNTR) from sequence data
stjudecloud/oliver
An opinionated Cromwell orchestration manager.
nextgenusfs/amptk
AMPtk: Amplicon ToolKit for NGS data (formally UFITS)