Mutual Software

Mutual is an algorithm that allows simultaneous transcriptome assembly of two related organisms to obtain predicted shared transcripts that appear in both organisms. It performs direct comparisons between paths in the two intermediate de Bruijn graph structures by an iterative extension strategy. Instead of utilizing coverage information, this strategy utilizes sequence similarity information within the paths that is often more reliable.

Installing Mutual

The Mutual software is available for download. The following steps will create a directory called mutual.

gunzip mutual.tar.gz
tar xvf mutual.tar
cd mutual
make

Add both <mutual_download_directory>/mutual and <mutual_download_directory>/mutual/bin to the search path.

Usage

Run Velvet and Oases for both organism A and organism B.

The current version of Mutual supports multi-threading through OpenMP.

Example:

velveth /home/velvetA 25 librariesA
velvetg /home/velvetA -read_trkg yes
oases /home/velvetA -cov_cutoff 3
velveth /home/velvetB 25 librariesB
velvetg /home/velvetB -read_trkg yes
oases /home/velvetB -cov_cutoff 3
mutual prefixa=/home/velvetA prefixb=/home/velvetB kmera=25 kmerb=25 blast_path=/home/blast

Parameters:

prefixa=/home/velvetA Velvet/Oases output directory for organism A
prefixb=/home/velvetB Velvet/Oases output directory for organism B
kmera=25 k-mer length in Velvet for organism A
kmerb=25 k-mer length in Velvet for organism B
blast_path=/home/blast path to BLAST directory (not BLAST+)
ini_e=1e-1 initial e-value cutoff (default 1e-1)
report_e=1e-7 reported e-value cutoff (default 1e-7)
threads=1 number of threads (default 1)
work_path=./ path to working directory (default ./)
saveintermediate=0 whether to save the intermediate results in working directory (0/1 for no/yes, default 0)

Output (in working directory):

outputa.fa predicted shared transcripts for organism A
outputb.fa predicted shared transcripts for organism B

The name of each transcript consists of its path in the de Bruijn graph followed by its best e-value.

Reference

Fu S., Tarone A.M. and Sze S.-H. (2015) Heuristic pairwise alignment of de Bruijn graphs to facilitate simultaneous transcript discovery in related organisms from RNA-Seq data. BMC Genomics, 16(Suppl 11), S5.