LACHESIS specifications

Information


Unique identifier OMICS_06670
Name LACHESIS
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for LACHESIS

LACHESIS in publications

 (5)
PMCID: 5802725
PMID: 29423238
DOI: 10.1038/s41438-017-0013-y

[…] scaffolding pipeline performed chromosome assignment and scaffold ordering and orientation on the contigs using the hi-c data as described previously,. proximo includes an enhanced version of the lachesis algorithm (http://shendurelab.github.io/lachesis/), along with a scaffold optimization algorithm, extra reports and qc steps. this method places contigs into chromosome groups based […]

PMCID: 5689209
PMID: 29145861
DOI: 10.1186/s12915-017-0439-6

[…] generate the sequence data (additional file : table s5)., whole genome alignment between the 33 mouse lemur super-scaffolds and 23 human chromosomes revealed that major portions of each mouse lemur lachesis group (ranging from 930 kb to 84.5 mb) shared sequence homology with either one or two of the 22 human autosomes and x chromosomes (additional file : figure s3). in light of this result, […]

PMCID: 5577786
PMID: 28854926
DOI: 10.1186/s12915-017-0412-4

[…] hi-c-based pe reads and used them to scaffold sra1 with proximotm (phase genomics), an adapted proximity-guided assembler based on the ligating adjacent chromatin enables scaffolding in situ (lachesis) assembler []. proximo clustered 92.1% (3240) of the short-read scaffolds, representing 99.6% (375.2 mb) of the total input sequence length, onto 16 large pseudomolecules to produce […]

PMCID: 4818521
PMID: 27036078
DOI: 10.1186/s12864-016-2596-3

[…] data sets generated using our rtcc protocol can provide a measurement of proximity between genomic elements in linear sense, allowing this knowledge to be used in bioinformatics applications such as lachesis for high quality genome assembly []., experiments were carried out with two c. elegans cultivars, each derived from the original wild type “n2” isolate used by brenner [], pd7052 is an n2 […]

PMCID: 4455782
PMID: 24855317
DOI: 10.1534/g3.114.011825

[…] m-y, not including p. pastoris; 18 for m-3d)., to scaffold the individual species’ genomes represented in each cluster of contigs, we aligned the hi-c reads to these contigs and ran them through our lachesis software () to create chromosome-scale scaffolds. the number of chromosomes in each species [7 for k. wickerhamii (); 8 for s. stipitis ()] was provided as an input to lachesis., […]


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LACHESIS institution(s)
Department of Genome Sciences, University of Washington, Seattle, WA, USA

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