Staphylococcus aureus:

1. shuffleSequences_fastq.pl frag_1.fastq frag_2.fastq frag.fastq
2. shuffleSequences_fastq.pl shortjump_1.fastq shortjump_2.fastq - | fastx_reverse_complement > shortjump.fastq
3. velveth . 31 -fastq -shortPaired frag.fastq -shortPaired2 shortjump.fastq
4. velvetg . -exp_cov auto -ins_length 180 -ins_length_sd 20 -ins_length2 3500 -ins_length2_sd 350 -scaffolding yes

Rhodobacter sphaeroides:

1. shuffleSequences_fastq.pl frag_1.fastq frag_2.fastq frag.fastq
2. shuffleSequences_fastq.pl shortjump_1.fastq shortjump_2.fastq - | fastx_reverse_complement > shortjump.fastq
3. velveth . 31 -fastq -shortPaired frag.fastq -shortPaired2 shortjump.fastq
4. velvetg . -exp_cov auto -ins_length 180 -ins_length_sd 20 -ins_length2 3500 -ins_length2_sd 350 -scaffolding yes

Human Chromosome 14:

1. shuffleSequences_fastq.pl frag_1.fastq frag_2.fastq frag.fastq
2. shuffleSequences_fastq.pl shortjump_1.fastq shortjump_2.fastq - | fastx_reverse_complement > shortjump.fastq
3. shuffleSequences_fastq.pl longjump_1.fastq longjump_2.fastq longjump.fastq
4. velveth . 31 -fastq -shortPaired frag.fastq -shortPaired2 shortjump.fastq -shortPaired3 longjump.fastq
5. velvetg . -exp_cov auto -ins_length 155 -ins_length_sd 15 -ins_length2 3000 -ins_length2_sd 300 -ins_length3 35000 -ins_length3_sd 3500 -scaffolding yes