SeqMap: mapping massive amount of oligonucleotides to the genome Hui Jiang et al. Bioinformatics (2008) 24: 2395-2396 The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next- generation sequencing Nathan Clement et al. Bioinformatics (2010) 26: 38-45 Presented by: Xia Li
12
Embed
SeqMap: mapping massive amount of oligonucleotides to the genome Hui Jiang et al. Bioinformatics (2008) 24: 2395-2396 The GNUMAP algorithm: unbiased probabilistic.
This document is posted to help you gain knowledge. Please leave a comment to let me know what you think about it! Share it to your friends and learn new things together.
Transcript
SeqMap: mapping massive amount of oligonucleotides to the genome
Hui Jiang et al. Bioinformatics (2008) 24: 2395-2396
The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides
from next-generation sequencing Nathan Clement et al. Bioinformatics (2010) 26: 38-45
Presented by: Xia Li
Short-read mapping software
Software Technique Reference
GNUMAPHashing refs + base quality + repeated regions Clement et al., 2010
Novoalign Hashing refs Novocraft, unpublished
SOAP Hashing refs Li et al., 2008
SeqMap Hashing reads Jiang et al., 2008
RMAP Hashing reads + read quality Smith et al., 2008
Eland Hashing reads Cox, unpublished
Bowtie BWT Langmead et al., 2009
Sliderlexicographically sorting + base quality Malhis et al., 2009
SeqMap
• Motivation– Hashing genome usually needs large memory (e.g.
SOAP needs 14GB memory when mapping to the human genome)