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Nawar Malhis et al.
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MOM: maximum oligonucleotide mapping
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ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches
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PASS: a program to align short sequences
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CloudBurst: highly sensitive read mapping with MapReduce
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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
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ZOOM! Zillions of oligos mapped
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SeqMap: mapping massive amount of oligonucleotides to the genome
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SOAP: short oligonucleotide alignment program
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Using quality scores and longer reads improves accuracy of Solexa read mapping
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Mapping short DNA sequencing reads and calling variants using mapping quality scores
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A space and time efficient algorithm for constructing compressed suffix arrays
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Space-efficient whole genome comparisons with Burrows-Wheeler transforms
RA Lippert
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