<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/34391?offset=190 https://bioinformaticsonline.com/bookmarks/view/44529/contigextender-a-new-approach-to-improving-de-novo-sequence-assembly-for-viral-metagenomics-data Wed, 08 May 2024 07:32:45 -0500 https://bioinformaticsonline.com/bookmarks/view/44529/contigextender-a-new-approach-to-improving-de-novo-sequence-assembly-for-viral-metagenomics-data <![CDATA[ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data]]> ContigExtender, was developed to extend contigs, complementing de novo assembly. ContigExtender employs a novel recursive Overlap Layout Candidates (r-OLC) strategy that explores multiple extending paths to achieve longer and highly accurate contigs. ContigExtender is effective for extending contigs significantly in in silico synthesized and real metagenomics datasets.

More at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7953547/

extension process

Address of the bookmark: https://github.com/dengzac/contig-extender

]]> LEGE https://bioinformaticsonline.com/bookmarks/view/35041/seal-sequence-alignment-evaluation-suite Wed, 03 Jan 2018 05:05:46 -0600 https://bioinformaticsonline.com/bookmarks/view/35041/seal-sequence-alignment-evaluation-suite <![CDATA[Seal: SEquence ALignment evaluation suite]]> Seal is a comprehensive sequencing simulation and alignment tool evaluation suite. This software (implemented in Java) provides several utilities that can be used to evaluate alignment algorithms, including:

  • Reading a pre-existing reference genome from one or more FASTA files.
  • Alternatively, generating an artificial reference genome based on input parameters (length, repeat count, repeat length, repeat variability rate).
  • Simulating reads from random locations in the genome based on input parameters of read length, coverage, sequencing error rate, and indel rate.
  • Applying alignment tools to the genome and the reads through a standardized interface.
  • Parsing the output of the alignment tool and calculating the number of reads that were correctly or incorrectly mapped.
  • Computing run times and measures of accuracy.

Seal has interfaces to evaluate the following software packages:

  • Bowtie
  • BWA
  • MAQ
  • mrFAST
  • mrsFAST
  • Novoalign
  • SHRiMP
  • SOAPv2

Address of the bookmark: http://compbio.case.edu/seal/

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