IDBA is the basic iterative de Bruijn graph assembler for second-generation sequencing reads. IDBA-UD, an extension of IDBA, is designed to utilize paired-end reads to assemble low-depth regions and use progressive depth on contigs to reduce errors in high-depth regions. It is a generic purpose assembler and epspacially good for single-cell and metagenomic sequencing data. See the IDBA home page for more info.
IDBA-UD can be run by the following command. Note that IDBA-UD requires paired-end reads stored in single FastA file and a pair of reads is in consecutive two lines. You can use fq2fa (part of the IDBA repository) to merge two FastQ read files to a single file. We have prepared such a FASTA formatted file called reads.fas. As our AWS instance has 16 cores, we use the option --num_threads 16 to tell IDBA-UD it should use 16 parallel threads. The log output will be redirected to file idba_ud.log:
cd /vol/spool/tutorial-data idba_ud -r reads.fas --num_threads 16 -o idba_ud_out >& idba_ud.log &
The contig sequences are located in the idba_ud_out directory in file contig.fa. Again, let's get some basic statistics on the contigs:
getN50.pl -s 500 -f idba_ud_out/contig.fa