Pseudo-it is a method developed by Brice Sarver( https://github.com/bricesarver/pseudo-it ). which generates a pseudoreference through a process of iterative mapping and reference calling steps. This project was designed to run on the TTU clusters but could easily be generalized for other environments.
Run pseudo-it-nextflow.pl without any parameters to see documentation.
TL;DR
ssh hrothgar
qlogin -pe sm 10 -q Yoda -P communitycluster
cd /lustre/scratch/my_project
nohup /lustre/work/daray/software/pseudo-it-nextflow-v0.4/pseudo-it-nextflow.pl
-reference /lustre/work/foobar/foo.fa
-PE1 /lustre/work/foobar/R1.fastq
-PE2 /lustre/work/foobar/R2.fastq
-SE /lustre/work/foobar/SE.fastq
-cluster hrothgar
-outputDir /lustre/scratch/username/results-genome1 >& run-genome1.log &
Release Notes:
0.4 : Initial release 0.5 : Added bwaBatchSize and haploBatchSize as command line parameters.
Robert Hubley, 2017