adaptive genome assembly using nanopore sequencing

A bioinformatic toolkit to align genome assemblies into pangenome graphs

GenomeTools genome analysis system.

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

Next generation sequencing reads de novo assembler.

Evaluating genome assemblies

map and call next generation genomic sequencing

parallelized blat with multi-threads support

Fast and accurately polish the genome generated by long reads.

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

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

A dotplot generator for large chromosomes

Machine-learning-based general bacterial promoter prediction tool.

Quick Indexing Compresssed FASTA tool

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

The Peaks software GitHub repository

blat with cluster parallel hybrid computing support

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

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

SMIS: Single Molecular Integrative Scaffolding