Post date: Oct 09, 2014 4:18:26 PM
I tried assembling the Sierra Nevada genome sequences with Platanus v1.2.1 (platanus). This program is supposed to work particularly well with samples with high heterozygosity. However, based on my results the genome is substantially underassembled relative to allpaths-lg, so I will stick with allpaths-lg. The assembly is in /labs/evolution/data/lycaeides/whole_genomes/platanusAssemblies and the script for the assembly is included below.
#!/bin/sh
#PBS -N platanus
#PBS -l nodes=1:ppn=48
#PBS -l walltime=96:00:00
#PBS -l mem=960g
#PBS -q batch
. /rc/tools/utils/dkinit
cd /labs/evolution/data/lycaeides/whole_genomes/platanusAssemblies
#platanus assemble -f sierra_180bp_1.fastq sierra_180bp_2.fastq -o sierra -k 32 -s 10 -n 0 -c 2 -a 10.0 -u 0.1 -d 0.5 -m 900 -t 44
#platanus scaffold -c sierra_contig.fa -b sierra_contigBubble.fa -IP1 sierra_180bp_1.fastq sierra_180bp_2.fastq -OP2 sierra_3kb_1.fastq sierra_3kb_2.fastq -o sierra -s 32 -v 32 -l 3 -u 0.1 -t 44
platanus gap_close -c sierra_contig.fa -IP1 sierra_180bp_1.fastq sierra_180bp_2.fastq -OP2 sierra_3kb_1.fastq sierra_3kb_2.fastq -o sierra -t 44