Assemble paired-end reads from single-cell or metagenomic sequencing technologies using the IDBA-UD assembler.
This is a KBase wrapper for the IDBA short read assembler.
IDBA-UD is an iterative graph-based assembler for single-cell and standard metagenomic short reads. IDBA-UD is an extension of IDBA algorithm and is good for data of highly uneven sequencing depth. In its assembly process, IDBA-UD iterates from a small k to a large k. In each iteration, short and low-depth contigs are removed using depth-relative cutoff thresholds, from low to high, to reduce the errors in low-depth and high-depth regions. This iterative approach compensates for the information loss with de Bruijn graphs constructed using a single kmer length. The reads are assembled locally to generate some missing k-mers in low-depth regions. For this reason, IDBA-UD is considered one of the more accurate microbial assemblers. IDBA-UD takes paired-end reads as input and generates an Assembly object as output.
IDBA version: 1.1.3.
- Peng Y, Leung HCM, Yiu SM, Chin FYL. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics. 2012;28: 1420 1428. doi:10.1093/bioinformatics/bts174 , https://academic.oup.com/bioinformatics/article/28/11/1420/266973
Module Commit: 22055be50fc510e9a63e53b4cfdb39ed59beef41