The MaSuRCA genome assembler

By Aleksey V. Zimin, Guillaume Marçais, Daniela Puiu, Michael Roberts, Steven L. Salzberg, James A. Yorke. Bioinform., 2013

1,277 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/476273d8efa79c3067e55bc5b556e34c88225491

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Citations in the corpus

Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads (2014, positive): “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.”
TGS-GapCloser: A fast and accurate gap closer for large genomes with low coverage of error-prone long reads (2020, positive): “TheseshortreadswereassembledusingMaSuRCA [23] (MaSuRCA, RRID:SCR 010691) version 3.3.1 or Mercedes (in-house tool) to obtain short but highly accurate contigs, and the SLR long-range (co-barcode/read cloud) and short-range (paired-end) information provided by the single-tube long fragment reads…”
Kraken: ultrafast metagenomic sequence classification using exact alignments (2014, methodology): “mers [17], and that process can be made faster through the caching behavior of the Kraken database.”
Piercing the dark matter: bioinformatics of long-range sequencing and mapping (2018, methodology): “Hybrid error correction methods, such as PBcR 32 , Nanocorr 33 , Spades 34 and MaSuRCA 35 , use short-read data to error correct the long reads before assembly and are especially effective when a limited amount of long-read coverage is available (typically below ~30× coverage) 32,33 .”
SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information (2014, result): “Similar observations were made for draft assemblies constructed from Illumina MiSeq reads with SPAdes [22] and MaSuRCA [23] (data not shown): the amount of contigs was lower or similar to that observed for CLCbio and Newbler, though the errors in the draft assembly led to more (erroneous) scaffolds.”
hybridSPAdes: an algorithm for hybrid assembly of short and long reads (2016, methodology): “Early tools for hybrid assembly combined Illumina and Sanger reads or Illumina and 454 reads (Boisvert et al., 2010; Chevreux et al., 1999; Zimin et al., 2013).”
ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter (2016, neutral): “In addition to the aforementioned assemblers, we also attempted to include ALLPATHS-LG 52488 (Gnerre et al. 2010) and MaSuRCA 3.1.3 (Zimin et al. 2013); however, we were unable to run these assemblers to completion on the HG004 data set (for details, see “ Assembler Scripts and Configuration Files…”