NextGenMap: Fast and accurate read mapping in highly polymorphic genomes
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Cites methods from "NextGenMap: Fast and accurate read ..."
...…al., 2012) to a modified pseudo-reference chromosome in which SNPs were inserted into the TAIR10 reference genome using NextGenMap (version 0.4.3; Sedlazeck et al., 2013) allowing up to 10% mismatch between the reads (-i 0.90) and the reference sequence and discarding reads that map equally well…...
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References
43,862 citations
"NextGenMap: Fast and accurate read ..." refers methods in this paper
...Representatives of BWT-based methods were BWA (Li and Durbin, 2009), its extension for longer reads BWA-SW (Li and Durbin, 2010) and Bowtie2 (Langmead and Salzberg, 2012)....
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...For low genomic polymorphism (0.1%), BWA-SW shows 0.1% and 0.2% more correctly mapped reads compared with NextGenMap for S1 and S2, respectively....
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...First, Burrows Wheeler transformation (BWT)-based methods, e.g. BWA (Li and Durbin, 2009), which are fast but optimized for short reads and genomes with low polymorphism....
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...If we compare the runtimes of the methods that showed the highest accuracy, NexGenMap is between 2.9 and 5.8 times faster than BWA-SW....
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37,898 citations
"NextGenMap: Fast and accurate read ..." refers methods in this paper
...Representatives of BWT-based methods were BWA (Li and Durbin, 2009), its extension for longer reads BWA-SW (Li and Durbin, 2010) and Bowtie2 (Langmead and Salzberg, 2012)....
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...NextGen Map’s CPU implementation was 1.1–2.3 times faster than Bowtie2, the fastest method so far....
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1,371 citations
"NextGenMap: Fast and accurate read ..." refers methods in this paper
...At the same time, NextGenMap outperforms current map- ping methods with respect to runtime and to the number of correctly mapped reads....
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1,184 citations
"NextGenMap: Fast and accurate read ..." refers methods in this paper
...As hash-based representative we selected Stampy (Lunter and Goodson, 2011)....
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...Second, hashbased methods like Stampy (Lunter and Goodson, 2011), which are slow but also suited for highly polymorphic genomes....
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305 citations