Fast gapped-read alignment with Bowtie 2
Citations
39,291 citations
Cites methods from "Fast gapped-read alignment with Bow..."
...To illustrate the value of data preprocessing, we evaluated two different scenarios: reference-based alignment using Bowtie 2 (Langmead and Salzberg, 2012) and BWA (Li and Durbin, 2009) against the Escherichia coli K-12/MG1655 reference (NCBI sequence NC_000913....
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13,192 citations
11,380 citations
Cites background or methods from "Fast gapped-read alignment with Bow..."
...Any reads not mapped in the previous stages (or mapped very poorly) are then re-aligned with Bowtie2 [15] against this novel transcriptome....
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...Indels due to sequencing errors will be discovered by Bowtie2 [15], the underlying mapping engine of TopHat2, which can detect short indels very efficiently....
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...TopHat2 can use either Bowtie [17] or Bowtie2 [15] as its core read-alignment engine....
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9,231 citations
8,090 citations
Cites methods from "Fast gapped-read alignment with Bow..."
...Bowtie2 and Cushaw2 are slower for 600bp reads (see Results)....
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...In this background, a few long-read alignment algorithms, notably including BWA-SW (Li and Durbin, 2010), Bowtie2 (Langmead and Salzberg, 2012), Cushaw2 (Liu and Schmidt, 2012) and GEM (Marco-Sola et al., 2012), have been developed....
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...On speed, BWA-MEM is similar to GEM and Bowtie2 for this data set, but is about 6 times as fast as Bowtie2 and Cushaw2 for a 650bp long-read data set....
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...We evaluated the performance of BWA-MEM on simulated data together with NovoAlign (http://novocraft.com), GEM, Bowtie2, Cushaw2, SeqAlto (Mu et al., 2012), BWA-SW and BWA (Figure 1)....
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References
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