The MaSuRCA genome assembler
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Cites methods from "The MaSuRCA genome assembler"
...mers [17], and that process can be made faster through the caching behavior of the Kraken database....
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Additional excerpts
...Furthermore, MaSuRCA required excessive execution time for assembly; for example, more than 1 mo in real time (using 32 threads) was required to assemble the oyster data....
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...We compared Platanus (version 1.2.1) with other major assemblers, including ALLPATHS-LG (Gnerre et al. 2011) (version 44837), MaSuRCA (Zimin et al. 2013) (version 2.0.4), Velvet (Zerbino and Birney 2008) (version 1.2.07), and SOAPdenovo2 (Luo et al. 2012) (version 2.04)....
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...MaSuRCA, the overlap-layoutconsensus–based assembler, did not undergo a sharp decrease in its scaffold NG50 in our simulation....
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...No significant reduction was observed in the corrected scaffold NG50 values from MaSuRCA, but the number of errors was approximately twofold greater in MaSuRCA than in Platanus for all heterozygosity levels. middle value (third) among the five assemblers assessed, and Platanus did not Platanus Genome Research 1389 www.genome.org decrease the number of mismatches and indels at the cost of its ‘N’ rate....
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...Velvet andMaSuRCA crashed during the execution of the runs (RAM: 512 GB; CPU: 32)....
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References
37,898 citations
"The MaSuRCA genome assembler" refers methods in this paper
...We mapped the reads to the finished sequence for the entire mouse genome using Bowtie2 (Langmead and Salzberg, 2012), allowing up to five best hits of identical quality for each read....
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22,269 citations
"The MaSuRCA genome assembler" refers background in this paper
...Received on May 20, 2013; revised on August 6, 2013; accepted on August 9, 2013...
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...…in coverage, SGS de novo assembly projects typically generate 100 times as many reads as Sanger-sequencing projects; e.g. the original human (Lander et al., 2001; Venter et al., 2001) and mouse (Mouse Genome Sequencing Consortium et al., 2002) projects generated 35 million reads each,…...
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16,859 citations
"The MaSuRCA genome assembler" refers background in this paper
...We supply the following four types of data to CABOG: (1) super-reads (2) linking mates (3) cleaned and de-duplicated jumping library mate pairs (if available) (4) other available LR We note that the modified version of CABOG 6.1 used in MaSuRCA is not capable of supporting the long high-error-rate reads generated by the PacBio technology....
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...TheMaSuRCA assembler benefits from the advanced assembly techniques in the CABOG assembler for creating contigs and scaffolds from super-reads....
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...We also compare the performance of MaSuRCA with the performance of CABOG only for the 9 Sanger data on the bacterial dataset....
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...CABOG uses read coverage statistics (Myers et al., 2000) to distinguish between unique and repetitive regions of the assembly....
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...The MaSuRCA assembler uses a modified version of the CABOG assembler for contiging and scaffolding, and in practice it will produce good assemblies with libraries whose standard deviations are up to 20% of the library mean....
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10,124 citations
9,389 citations
"The MaSuRCA genome assembler" refers methods in this paper
...Recently developed assemblers that use the de Bruijn strategy include Allpaths-LG (Gnerre et al., 2010), SOAPdenovo (Li et al., 2008), Velvet (Zerbino and Birney, 2008), EULER-SR (Chaisson and Pevzner, 2008) and ABySS (Simpson et al., 2009)....
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...…by guest on 03 M arch 2019 Bambus2 (Koren et al., 2011) CABOG (Miller et al., 2008) MSR-CA (now renamed MaSuRCA 1.0) SGA (Simpson and Durbin, 2012) SOAPdenovo (Luo et al., 2012) Velvet (Zerbino and Birney, 2008) The best performers in GAGE were AllPaths-LG and SOAPdenovo....
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...The original GAGE assembly comparison (Salzberg et al., 2012) compared the following assembly programs: ABySS (Simpson et al., 2009) ALLPATHS-LG (Gnerre et al., 2011) D ow nloaded from https://academ ic.oup.com /bioinform atics/article-abstract/29/21/2669/195975 by guest on 03 M arch 2019 Bambus2 (Koren et al., 2011) CABOG (Miller et al., 2008) MSR-CA (now renamed MaSuRCA 1.0) SGA (Simpson and Durbin, 2012) SOAPdenovo (Luo et al., 2012) Velvet (Zerbino and Birney, 2008) The best performers in GAGE were AllPaths-LG and SOAPdenovo....
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..., 2008), Velvet (Zerbino and Birney, 2008), EULER-SR (Chaisson and Pevzner, 2008) and ABySS (Simpson et al....
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...3.0 (Bankevich et al., 2012) and Velvet....
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