Quick Indexing Compresssed FASTA tool

blat with cluster parallel hybrid computing support

bvSFM (bit-vector sampled FM-index) is a tool for sequence alignment.

The Peaks software GitHub repository

SMIS: Single Molecular Integrative Scaffolding. A pipeline for scaffolding genome assemblies using long reads (PacBio, ONT)

Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads.

SMIS: Single Molecular Integrative Scaffolding

Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads

map and call next generation genomic sequencing

adaptive genome assembly using nanopore sequencing

A tool for compression and analysis of DNA sequences

A dotplot generator for large chromosomes

A bioinformatic toolkit to align genome assemblies into pangenome graphs

Machine-learning-based general bacterial promoter prediction tool.

Evaluating genome assemblies

parallelized blat with multi-threads support

An efficient index for the colored, compacted, de Bruijn graph

a python package for fast random access to sequences from plain and gzipped FASTA/Q files

Fast and accurately polish the genome generated by long reads.

GenomeTools genome analysis system.