Examples


Data sets

1. Human Genome (HG18 - hg18.fa)

hg76_500k.fastq: 500k single-end reads of length 76bp.
- We picked the fist 500k reads from DRR000617_1.fastq.

hg100_1m.fastq: 1 million single-end reads of length 100bp.
- We picked the first 1 million reads from SRR062634_1.filt.fastq.

hg100_1m_pe1.fq & hg100_1m_pe2.fq: 1 million paired-end reads of length 100bp.
- We picked the first 1 million pairs of reads from SRR062634_1.filt.fastq & SRR062634_2.filt.fastq

2. Caenorhabdities Elegans (WormBase WS201 - ce.fa)

ce100_1m.fastq: 1 million single-end reads of length 100bp.
- We picked the first 1 million reads from SRR065390_1.fastq

3. Drosophila Melanogaster (FlyBase release 5.42 - dm.fa)

dm100_1m.fastq: 1 million single-end reads of length 100bp for D. melanogaster
- We picked the first 1 million reads from SRR497711_1.fastq


Constructing Hobbes Indexes

HG18
./hobbes-index --sref hg18.fa -i hg18.hix -g 11 -p 4

C. elegans
./hobbes-index --sref ce.fa -i ce.hix -g 11 -p 4

D. melanogaster
./hobbes-index --sref dm.fa -i dm.hix -g 11 -p 4


Running Hobbes for Single-End Reads

1. Edit Distance

genome = HG18, read length = 100bp, # of reads = 1 million, threshold = 5
./hobbes -q hg100_1m.fastq --sref hg18.fa -i hg18.hix -a --indel -v 5 -n 1000000 -p 1 > out.sam
./hobbes -q hg100_1m.fastq --sref hg18.fa -i hg18.hix -a --indel -v 5 -n 1000000 -p 16 > out.sam

genome = C. elegans, read length = 100bp, # of reads = 1 million, threshold = 5
./hobbes -q ce100_1m.fastq --sref ce.fa -i ce.hix -a --indel -v 5 -n 1000000 -p 1 > out.sam
./hobbes -q ce100_1m.fastq --sref ce.fa -i ce.hix -a --indel -v 5 -n 1000000 -p 16 > out.sam

genome = D. melanogaster, read length = 100bp, # of reads = 1 million, threshold = 5
./hobbes -q dm100_1m.fastq --sref dm.fa -i dm.hix -a --indel -v 5 -n 1000000 -p 1 > out.sam
./hobbes -q dm100_1m.fastq --sref dm.fa -i dm.hix -a --indel -v 5 -n 1000000 -p 16 > out.sam

2. Hamming Distance

genome = HG18, read length = 76bp, # of reads = 500k, threshold = 3
./hobbes -q hg76_500k.fastq --sref hg18.fa -i hg18.hix -a --hamming -v 3 -n 500000 -p 1 > out.sam
./hobbes -q hg76_500k.fastq --sref hg18.fa -i hg18.hix -a --hamming -v 3 -n 500000 -p 16 > out.sam

genome = HG18, read length = 100bp, # of reads = 500k, threshold = 5
./hobbes -q hg100_1m.fastq --sref hg18.fa -i hg18.hix -a --hamming -v 5 -n 500000 -p 1 > out.sam
./hobbes -q hg100_1m.fastq --sref hg18.fa -i hg18.hix -a --hamming -v 5 -n 500000 -p 16 > out.sam


Running Hobbes for Paired-End Reads

1. Edit Distance

genome = HG18, read length = 100bp, # of reads = 1 million, threshold = 5
./hobbes --pe --seqfq1 hg100_1m_pe1.fq --seqfq2 hg100_1m_pe2.fq --sref hg18.fa -i hg18.hix -a --indel -v 5 --min 110 --max 290 -n 1000000 -p 1 > out.sam
./hobbes --pe --seqfq1 hg100_1m_pe1.fq --seqfq2 hg100_1m_pe2.fq --sref hg18.fa -i hg18.hix -a --indel -v 5 --min 110 --max 290 -n 1000000 -p 16 > out.sam

2. Hamming Distance

genome = HG18, read length = 100bp, # of reads = 500k, threshold = 5
./hobbes --pe --seqfq1 hg100_1m_pe1.fq --seqfq2 hg100_1m_pe2.fq --sref hg18.fa -i hg18.hix -a --hamming -v 5 --min 110 --max 290 -n 500000 -p 1 > out.sam
./hobbes --pe --seqfq1 hg100_1m_pe1.fq --seqfq2 hg100_1m_pe2.fq --sref hg18.fa -i hg18.hix -a --hamming -v 5 --min 110 --max 290 -n 500000 -p 16 > out.sam


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