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An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

File and Archive Manager

Accelerated BLAST compatible local sequence aligner.

SPAdes Genome Assembler

A fast and sensitive gapped read aligner

A single molecule sequence assembler for genomes large and small.

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Ultra-fast and memory-efficient (meta-)genome assembler

a Bioinformatics Application for Navigating De novo Assembly Graphs Easily

hybrid assembly pipeline for bacterial genomes

Signal-level algorithms for MinION data

Mummer alignment tool

SeqAn's official repository.

Fast Whole-Genome Similarity (ANI) Estimation

adapter trimmer for Oxford Nanopore reads

quality filtering tool for long reads

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

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which wil…

A fast approximate aligner for long DNA sequences

Optimized Dynamic Genome/Graph Implementation: understanding pangenome graphs

A gap-closing software tool that uses long reads to enhance genome assembly.

The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.

A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.

Scalable annotated de Bruijn graphs for DNA indexing, alignment, and assembly

MetaMDBG: a lightweight assembler for long and accurate metagenomics reads.

SIMD partial order alignment tool/library

Assembled Genomes Compressor

Short-read and long-read sequencing tools for diagnostics