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Konnector specifications

Information


Unique identifier OMICS_07352
Name Konnector
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 1.5.2
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Rene Warren <>

Konnector in publications

 (5)
PMCID: 5748696
PMID: 29232881
DOI: 10.3390/genes8120378

[…] assembled paired-end reads from the non-partitioned libraries from both of the individuals. briefly, paired-end sequences from the same individual as the partitioned library were processed using konnector (version 2.0) [], which performs local de bruijn graph assembly to generate pseudo-long reads representing complete dna fragments. the resulting pseudo-long reads and remaining sequence […]

PMCID: 5748697
PMID: 29232880
DOI: 10.3390/genes8120379

[…] instructions. the initial assembly was 2.394 gbp with a genomic scaffold n50 length of 21.34 mbp (). improvements to the initial assembly were made by incorporating local assemblies using konnector (version 2.0) [], which attempts to fill the intervening gap between two paired sequences from a library fragment to provide longer sequences useful for scaffolding. partitioned […]

PMCID: 5681567
PMID: 29127278
DOI: 10.1038/s41467-017-01316-7

[…] of ram and dual intel xeon x-5550 2.67 ghz cpus running red hat enterprise linux 5 as part of westgrid, compute canada., pet read pairs were merged sequentially using the abyss-mergepairs tool and konnector (version 1.9.0). bloom filters were constructed from all reads using the abyss-bloom utility, and every tenth value of k between 75 and 245 bp, inclusive. reads from potentially mixed […]

PMCID: 5596377
PMID: 28898352
DOI: 10.1590/1678-4685-GMB-2016-0230

[…] although can be applied in small prokaryote genomes as well. the main algorithm consists in the selection of nucleotides in the assembly that flank the gap-regions, followed by a local assembly by konnector () using data from paired-end reads. konnector, which takes the paired-end reads and generates pseudo-long reads by applying a combination of bloom filter and de bruijn graph, […]

PMCID: 5025161
PMID: 27632164
DOI: 10.1371/journal.pone.0163059

[…] the white spruce chloroplast sequence, we determined that our scaffold was missing around 40 bp of sequence at the 5' end, and 2 kb of sequence at the 3' end. to recover these missing bases, we used konnector [], which fills in nucleotides between paired-end reads given a bloom filter representation of a de bruijn graph. since we expected the chloroplast genome to be circular, we supplied the 5’ […]


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