LongStitch¶

Description¶

LongStitch is a genome assembly correction and scaffolding pipeline that leverages long read sequencing data through a multi stage process—using Tigmint long to fix misassemblies, ntLink to scaffold, and optionally ARKS long for further enhancement.

Environment Modules¶

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

Environment Variables¶

HPC_LONGSTITCH_DIR - installation directory
HPC_LONGSTITCH_BIN - executable directory

Citation¶

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

Categories¶

genomics, biology