Purge haplotigs

From UFRC
Revision as of 14:19, 27 July 2022 by Dgalliera (talk | contribs) (Created page with "Category:Software Category:Sequencing Category:Bioinformatics Category:Biology {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|purge_haplotigs}} |{{#vardefi...")
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to navigation Jump to search

Description

purge_haplotigs website  

Purge_haplotigs is designed to identify pairs of contigs that are syntenic and move one of them to the haplotig 'pool'. The pipeline uses mapped read coverage and Minimap2 alignments to determine which contigs to keep for the haploid assembly. Dotplots are optionally produced for all flagged contig matches, juxtaposed with read-coverage, to help the user determine the proper assignment of any remaining ambiguous contigs. The pipeline will run on either a haploid assembly (i.e. Canu, FALCON or FALCON-Unzip primary contigs) or on a phased-diploid assembly (i.e. FALCON-Unzip primary contigs + haplotigs). Here are two examples of how Purge Haplotigs can improve a haploid and diploid assembly.

Environment Modules

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

System Variables

  • HPC_PURGE_HAPLOTIGS_DIR - installation directory




Citation

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

The pipeline is published at BMC Bioinformatics:

Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies