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longstitch website  

A genome assembly correction and scaffolding pipeline using long reads, consisting of up to three steps:

  • Tigmint cuts the draft assembly at potentially misassembled regions
  • ntLink is then used to scaffold the corrected assembly
  • followed by ARKS for further scaffolding (optional extra step of scaffolding)

Environment Modules

Run module spider longstitch to find out what environment modules are available for this application.

System Variables

  • HPC_LONGSTITCH_DIR - installation directory
  • HPC_LONGSTITCH_BIN - executable directory


If you publish research that uses longstitch you have to cite it as follows:

Coombe L, Li JX, Lo T, Wong J, Nikolic V, Warren RL and Birol I. LongStitch: high-quality genome assembly correction and scaffolding using long reads. BMC Bioinformatics 22, 534 (2021). https://doi.org/10.1186/s12859-021-04451-7