Short Sequence Assembly by K-mer search and 3' read Extension (SSAKE) 

SSAKE v3.8.2 Rene L. Warren, 2006-2014
email: rwarren at bcgsc.ca

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Campylobacter showae CC57C (colorectal cancer tumor isolate)
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The assembly of ~1M quality-trimmed (../tools/TQSfastq.py -f Assemble_1_R1.fastq -t 30 -c 100 -e 33) Campylobacter showae CC57C (BioProject/Accession:PRJNA189774/AOTD00000000) bacterial NGS reads (1 lane, Illumina MiSeq, PE151, 1.8M pairs sequenced) with SSAKE v3.8.2 in paired-end mode took 10m31s and 3.8GB RAM on a 12-core 48GB RAM CentOS5 machine (Benchmark with syrupy @https://github.com/jeetsukumaran/Syrupy) and yielded 215 contigs with N50=41kbp (151 scaffolds, N50=124kbp), and a reconstruction of 2.2Mbp. 

Quality-Trimmed CC57C Illumina MiSeq sequence data available here:

ftp://ftp.bcgsc.ca/supplementary/SSAKE/CC57C_paired.fa and CC57C_unpaired.fa

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SSAKE ASSEMBLY PIPELINE:
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./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
./tools/makePairedOutput2UNEQUALfiles.pl Assemble_1_R1.fastq_T30C100E33.trimFIX.fa Assemble_1_R2.fastq_T30C100E33.trimFIX.fa 400
./SSAKE -f CC57C_paired.fa -p 1 -g CC57C_unpaired.fa -m 20 -w 5 -b run2014
./ssake_v3-8-2/tools/getStats.pl run2014.contigs

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SSAKE CONTIG SEQUENCE STATS
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Mean (nt),10476.89
Max (nt),119107
Min (nt),200
n,215
Stdev (nt),19021.54
Variance (nt),361818996.83
TrimmedMean (nt),2763.44
Median (nt),412.00
Sum (nt),2252531.00
N20,64969
N50,41436
N80,17465
Size Range,#bases,#sequences
>=100000,119107,1
10000-100000,1951445,63
200-1000,36330,119
1000-10000,145649,32

./ssake_v3-8-2/tools/makeFastaFileFromScaffolds.pl run2014.scaffolds
./ssake_v3-8-2/tools/getStats.pl run2014.scaffolds.fa

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SSAKE SCAFFOLD SEQUENCE STATS
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Mean (nt),14931.05
Max (nt),252560
Min (nt),200
n,151
Stdev (nt),42086.22
Variance (nt),1771250106.52
TrimmedMean (nt),349.95
Median (nt),288.00
Sum (nt),2254589.00
N20,227805
N50,124387
N80,59173
Size Range,#bases,#sequences
>=100000,1350704,8
10000-100000,805378,18
200-1000,33684,113
1000-10000,63291,12