Post date: Feb 11, 2015 7:25:25 PM
I am using mugsy to align the Lycaeides whole genomes to each other. Mugsy relies heavily on mummer, which it uses for pairwise alignments. Information on running the program (there are few to no options) can be found here: http://mugsy.sourceforge.net/. Some modifications might be possible via the perl wrapper scripts that are part of the program, look in http://mugsy.sourceforge.net/. Here is the bash script I used to start the job (running on lycaeides-k0623):
#!/bin/sh
#PBS -N genome
#PBS -l nodes=1:ppn=16
#PBS -l walltime=240:00:00
#PBS -l mem=960g
#PBS -q long
bash
source /labs/evolution/Source/mugsy_x86-64-v1r2.3/mugsyenv.sh
mkdir /local/scratch/mugsy
mugsy --directory /local/scratch/mugsy --prefix mugsyLycaeides /labs/evolution/data/lycaeides/whole_genomes/Lanna/DATA/RUN/ASSEMBLIES/assem18sept14/LannaFinalAssembly.fasta /labs/evolution/data/lycaeides/whole_genomes/Lidas/DATA/RUN/ASSEMBLIES/assem9oct14/LidasFinalAssembly.fasta /labs/evolution/data/lycaeides/whole_genomes/Lmelissa/DATA/RUN/ASSEMBLIES/assem22sept14/Lmelissa2FinalAssembly.fasta /labs/evolution/data/lycaeides/whole_genomes/Lsierra/DATA/RUN/ASSEMBLIES/assem15sept14/LsierraFinalAssembly.fasta /labs/evolution/data/lycaeides/whole_genomes/Lwarner/DATA/RUN/ASSEMBLIES/assem12oct14/LwarnerFinalAssembly.fasta /labs/evolution/data/lycaeides/melissa_genome/Lmelissa1FinalAssembly.fasta
rsync -avz /local/scratch/mugsy /labs/evolution/data/lycaeides/whole_genomes/mugsyGenomeAlgns/