/usr/share/doc/ssake/examples/MiSeqCampylobacterAssemblyPIPELINE.sh is in ssake-examples 4.0-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 | #!/bin/sh
d=`date`
echo -----------------------------------------------------------------------------------
echo Running SSAKE assembly pipeline on bacterial sequence data.
echo -----------------------------------------------------------------------------------
echo Downloading MiSeq data for Campylobacter showae CC57C on $d ...
echo -----------------------------------------------------------------------------------
rm -rf Assemble_1_R*.fastq
wget ftp://ftp.bcgsc.ca/supplementary/SSAKE/Assemble_1_R*.fastq
echo -----------------------------------------------------------------------------------
echo done. Trimming low quality bases, be patient...
echo -----------------------------------------------------------------------------------
../tools/TQSfastq.py -f Assemble_1_R1.fastq -t 30 -c 100 -e 33
../tools/TQSfastq.py -f Assemble_1_R2.fastq -t 30 -c 100 -e 33
cat Assemble_1_R2.fastq_T30C100E33.trim.fa |perl -ne 'if(/^(\>\@\S+)/){print "$1b\n";}else{print;}' >Assemble_1_R2.fastq_T30C100E33.trimFIX.fa
cat Assemble_1_R1.fastq_T30C100E33.trim.fa |perl -ne 'if(/^(\>\@\S+)/){print "$1a\n";}else{print;}' >Assemble_1_R1.fastq_T30C100E33.trimFIX.fa
echo -----------------------------------------------------------------------------------
echo done. Formatting fasta input for SSAKE...
echo -----------------------------------------------------------------------------------
../tools/makePairedOutput2UNEQUALfiles.pl Assemble_1_R1.fastq_T30C100E33.trimFIX.fa Assemble_1_R2.fastq_T30C100E33.trimFIX.fa 400
echo -----------------------------------------------------------------------------------
echo done. Initiating SSAKE assembly ETA 10-20min depending on system...
echo -----------------------------------------------------------------------------------
time ../SSAKE -f paired.fa -p 1 -g unpaired.fa -m 20 -w 5 -b Cshowae
echo -----------------------------------------------------------------------------------
echo done. Computing stats from contigs
echo -----------------------------------------------------------------------------------
../tools/getStats.pl Cshowae_contigs.fa 500 > Cshowae_contigs_stats.fa
echo done. Computing stats from scaffolds
echo -----------------------------------------------------------------------------------
../tools/getStats.pl Cshowae_scaffolds.fa 500 > Cshowae_scaffolds_stats.txt
echo assembly pipeline complete. Results are under Cshowae.
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