Staphylococcus aureus, Rhodobacter sphaeroides & Human Chromosome 14:

1. sga preprocess -p 1 frag_?.fastq > frag.pp.fa
2. sga index -t 20 frag.pp.fa
3. sga correct -k 31 -t 20 frag.pp.fa -o frag.pp.ec.fa
4. sga index -t 31 frag.pp.ec.fa
5. sga filter frag.pp.ec.fa
6. sga overlap -t 20 –m 45 frag.pp.ec.filter.pass.fa
7. sga assemble frag.pp.ec.filter.pass.asqg.gz
8. ln -s default-contigs.fa genome.ctg.fasta
9. sga-align --name frag genome.ctg.fasta frag_?.fastq
10. sga-align --name shortjump genome.ctg.fasta shortjump_?.fastq
11. sga-bam2de.pl -n 5 --prefix frag frag.bam
12. sga-astat.py -m 200 frag.refsort.bam > genome.ctg.astat
13. sga-bam2de.pl -n 5 --prefix shortjump shortjump.bam
14. sga scaffold -m 200 --pe frag.de --mate-pair shortjump.de -a genome.ctg.astat -o genome.scaf genome.ctg.fasta
15. sga scaffold2fasta -m 200 -f genome.ctg.fasta -o genome.scf.fasta genome.scaf --write-unplaced --use-overlap