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next-generation-sequencing

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ablab /spades

SPAdes Genome Assembler

sequencing next-generation-sequencing illumina genome-assembly sequence-assembler transcriptome-assembly metagenome-assembly

UpdatedOct 13, 2025
C++

jvarkit

lindenb /jvarkit

Java utilities for Bioinformatics

java science bioinformatics genomics biology ngs next-generation-sequencing

UpdatedOct 15, 2025
Java

nf-core /sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

workflow bioinformatics pipeline annotation genomics nextflow cancer reproducible-research containers conda next-generation-sequencing variant-calling somatic germline whole-exome-sequencing whole-genome-sequencing pre-processing nf-core gatk4 target-panels

UpdatedNov 5, 2025
Nextflow

openbiox /awosome-bioinformatics

A curated list of resources for learning bioinformatics.

bioinformatics next-generation-sequencing data-analysis

UpdatedFeb 23, 2022

sanger-pathogens /Roary

Rapid large-scale prokaryote pan genome analysis

bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases

UpdatedNov 3, 2025
Perl

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

docker mapper next-generation-sequencing alignment long-read pacbio bioconda oxford-nanopore structural-variations

UpdatedMar 18, 2024
C++

bioinformatics-centre /kaiju

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database

bioinformatics taxonomy next-generation-sequencing metagenomics taxonomic-classification

UpdatedApr 25, 2025
C

sanger-pathogens /snp-sites

Finds SNP sites from a multi-FASTA alignment file

bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases

UpdatedDec 16, 2020
C

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

bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases

UpdatedJun 15, 2024
Java

sanger-pathogens /circlator

A tool to circularize genome assemblies

bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases

UpdatedApr 6, 2024
Python

nextstrain /nextclade

Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement

science research virus sequencing next-generation-sequencing dna rna influenza sequences strain nextstrain ncov coronavirus covid-19 covid covid19 sars-cov-2 neherlab clades clade

UpdatedNov 3, 2025
TypeScript

nickjcroucher /gubbins

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases

UpdatedAug 27, 2025
Python

sanger-pathogens /ariba

Antimicrobial Resistance Identification By Assembly

bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases

UpdatedOct 12, 2023
Python

ngless-toolkit /ngless

NGLess: NGS with less work

science haskell bioinformatics genomics ngs next-generation-sequencing metagenomics bioinformatics-pipeline fastq-format fastq haskell-language samtools bwa

UpdatedMar 19, 2025
Haskell

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

UpdatedJan 26, 2022
C++

alastair-droop /fqtools

An efficient FASTQ manipulation suite

bioinformatics next-generation-sequencing fastq fastq-files

UpdatedJan 27, 2020
C

Sarek

SciLifeLab /Sarek

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

docker workflow bioinformatics pipeline genomics nextflow cancer somatic-variants reproducible-research containers next-generation-sequencing singularity reproducible-science somatic germline germline-variants

UpdatedJan 27, 2020
Nextflow

sanger-pathogens /assembly-stats

Get assembly statistics from FASTA and FASTQ files

bioinformatics research genomics pathogen sequencing next-generation-sequencing global-health infectious-diseases

UpdatedMay 9, 2023
C++

SNPGenie

chasewnelson /SNPGenie

Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data

evolution perl next-generation-sequencing vcf population-genetics dnds-estimation molecular-evolution nucleotide fasta-sequences vcf-files diversity-measurement sequence-analysis dnds natural-selection snp-report nucleotide-diversity evolutionary-parameters substitution-rate nei-gojobori

UpdatedAug 21, 2023
Perl

xjtu-omics /msisensor-pro

Microsatellite Instability (MSI) detection using high-throughput sequencing data.

next-generation-sequencing hypermutation microsatellite-instability dna-missmatch-repair-system tumor-only-support

UpdatedApr 2, 2025
C++

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