Module: rje_mashmap Description: MashMap control and parsing module Version: 0.0.0 Last Edit: 19/11/21

Copyright © 2021 Richard J. Edwards - See source code for GNU License Notice

Imported modules: rje rje_obj rje_db

See SLiMSuite Blog for further documentation. See rje for general commands.

Function

This module will run MashMap on two assemblies and have the code for additional parsing and filtering methods where appropriate.

Commandline

Main MashMap run options

seqin=FILE : Genome assembly used as the query (also recognises assembly=FILE) []
reference=FILE : Genome assembly used as the searchdb (also refgenome=FILE or searchdb=FILE) []
basefile=X : Prefix for output files [$SEQIN.$REFERENCE]
threads=INT : Number of threads to use for MashMap runs []
seglength=INT : MashMap segment length (--seqLength <value>) [1000]
mashpid=NUM : MashMap threshold for identity [85]
mashfilt=X : MashMap filtering mode (map/both/none; both=one-to-one) [both]

MashMap filtering options

selfhit=T/F : Whether to include self hits (matching name, pos, strand) [True]
minloclen=INT : Minimum length for aligned chunk to be kept (shortest hit length in bp) [1000]
minlocid=PERC : Minimum percentage identity for aligned chunk to be kept (local %identity) [50]

History Module Version History

    # 0.0.0 - Initial Compilation.