added pbs script for command testing

Author: ryanmelnyk

assemble.pbs

@@ -0,0 +1,19 @@
+#!/bin/bash
+#PBS -r n
+#PBS -N Assemble409
+#PBS -l walltime=100:00:00
+#PBS -l procs=8
+#PBS -l pmem=16000m
+#!/bin/bash
+file=assemblies/CH409
+
+# scythe -a adapters/illumina_adapters.fa $file.1.fastq -o $file.scythed.1.fastq -q sanger
+# scythe -a adapters/illumina_adapters.fa $file.2.fastq -o $file.scythed.2.fastq -q sanger
+#
+# sickle pe -f $file.scythed.1.fastq -r $file.scythed.2.fastq -o $file.sickled.1.fastq -p $file.sickled.2.fastq -s $file.singles.fastq -t sanger
+#
+# pear -f $file.sickled.1.fastq -r $file.sickled.2.fastq -o $file -j 8
+#
+# cat $file.singles.fastq $file.assembled.fastq > $file.all.singles.fastq
+
+spades.py -m 16 -s $file.all.singles.fastq -1 $file.unassembled.forward.fastq -2 $file.unassembled.reverse.fastq --careful --cov-cutoff auto -t 8 -o $file