SCUBAT2 (Scaffolding Contigs Using BLAST And Transcripts v2) uses transcriptome or proteome information to scaffold the genome. It was inspired by the original SCUBAT algorithm by Ben Elsworth.

Biopython - to parse BLAST XML file

Numpy - to calculate some statistics

Requires a BLAST XML file

blastn -query transcripts.fa -db contigs.fa -evalue 1e-25 -outfmt 5 -out blast.xml

For the same species the default settings for identity cutoff should be okay

The user must specify the max allowed intron size (i.e for nematode species ~ 20000 bp). Alternatively the user can run the program with --intron_size_run that creates the file intron_size which has the intron sizes calculated by the mapped transcripts

Example command

SCUBAT_v2.py -b [blast.xml] -f [assembly.file] -max 20000