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MECAT is a tool for de novo assembly of long single molecule sequenced reads (e.g. PacBio). The tool implemented a pseudolinear alignment scoring algorithm to remove unnecessary alignments based on distance difference factors (DDFs) to score matched k-mer pairs. Large genomes can be assembled on a single computer using this tool.


Sequence assembly


  • Operation: Sequence assembly; De-novo assembly
  • Input: FASTA; FASTQ
  • Output: -
  • Software interface: Command-line user interface
  • Language: C++;C;Perl
  • Operating system: Linux; Mac OS X
  • License: GPLv3
  • Cost: Free
  • Version name: -
  • Credit: National Natural Science Foundation of China
  • Contact: xiaochuanle _at_;chenying2016 _at_;luofeng _at_
  • Collection: -


Xiao CL, Chen Y, Xie SQ, Chen KN, Wang Y, Han Y, Luo F, Xie Z "MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads." Nat Methods. 2017 Nov;14(11):1072-1074. 18.
PMID: 28945707

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