IDBA-MT¶

Description¶

IDBA-MT is an iterative De Bruijn Graph De Novo short read assembler for meta-transcriptome. It is purely de novo assembler based on paired-end RNA sequencing reads only. IDBA-MT is a post-processing software for IDBA-UD contigs for removing chimeria contigs and extending contig length using paired-end reads information. IDBA-MTP is an optional pre-processing software for IDBA-MT. It generates candidate contigs by aligning reference protein sequences to de Bruijn graph. Please run IDBA-UD and IDBA-MT after running IDBA-MTP to get confident result.

Environment Modules¶

Run module spider idba-mt to find out what environment modules are available for this application.

Environment Variables¶

HPC_IDBA_MT_DIR - installation directory
HPC_IDBA_MT_BIN - executable directory
HPC_IDBA_MT_DOC - documentation directory

Categories¶

biology, ngs