The GEM mapper: fast, accurate and versatile alignment by filtration
Citations
14,103 citations
8,090 citations
Cites methods from "The GEM mapper: fast, accurate and ..."
...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....
[...]
...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....
[...]
...While GEM is both fast and accur te for up to approximately 1000bp reads, it mandates end-to-end alignment and does not perform affine-gap alignment, which limits its uses for long-read alignment....
[...]
...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)....
[...]
...BWA-MEM is close to NovoAlign for PE reads and is comparable to GEM and Cushaw2 for SE....
[...]
2,228 citations
Cites background from "The GEM mapper: fast, accurate and ..."
...Most aligners then work out from the location that the seed mapped to, trying to match the remainder of the read to the genome surrounding the original location, a process often called the extension step (2)....
[...]
1,963 citations
Cites background from "The GEM mapper: fast, accurate and ..."
...[204]), achieve ultra-fast mapping (GEM [205]) or map long-reads...
[...]
1,892 citations
References
45,957 citations
43,862 citations
37,898 citations
20,335 citations
7,023 citations