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Kollector is a tool for assembling gene sequences based on the assembler ABySS by using transcript sequences as baits to capture whole genome shotgun (WGS) reads. This way, the WGS reads used for assembly are specific to the genomic region. The algorithm identifies kmers from transcripts and seed them to a progressive bloom filter, which is needed to gather genes among WGS reads.


Sequence assembly


  • Operation: Sequence assembly; Localised reassembly
  • Input: FASTA
  • Output: FASTA
  • Software interface: Command-line user interface
  • Language: Bash
  • Operating system: Linux; Mac OS X
  • License: GPLv3
  • Cost: Free
  • Version name: -
  • Credit: National Institutes of Health; Genome Canada
  • Contact: ibirol _at_
  • Collection: -


Kucuk E, Chu J, Vandervalk BP, Hammond SA, Warren RL, Birol I "Kollector: transcript-informed, targeted de novo assembly of gene loci." Bioinformatics. 2017 Jun 15;33(12):1782-1788.
PMID: 28186221
PMCID: PMC5572715

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