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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 citations

 (6)
library_books

Chromosome scale scaffolding of the black raspberry (Rubus occidentalis L.) genome based on chromatin interaction data

2018
PMCID: 5802725
PMID: 29423238
DOI: 10.1038/s41438-017-0013-y

[…] i-C 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 on the st […]

library_books

Hybrid de novo genome assembly and centromere characterization of the gray mouse lemur (Microcebus murinus)

2017
BMC Biol
PMCID: 5689209
PMID: 29145861
DOI: 10.1186/s12915-017-0439-6

[…] ) FASTA file generation.We performed two rounds of BNG conflict-resolution and hybrid scaffolding to identify and resolve putative scaffolding conflicts in both our primary Mmur 2.0 assembly and post Lachesis round 1 assembly (e.g., to resolve putative misassemblies introduced by Hi-C cross-chromosome 3D interactions). This iterative approach provided greater confidence in the long-range scaffoldi […]

library_books

Single molecule sequencing and Hi C based proximity guided assembly of amaranth (Amaranthus hypochondriacus) chromosomes provide insights into genome evolution

2017
BMC Biol
PMCID: 5577786
PMID: 28854926
DOI: 10.1186/s12915-017-0412-4

[…] caffolds from the SRA1 were retained for downstream analyses. Scaffolds from the SRA1 were clustered, ordered, and oriented using ProximoTM, an adapted proximity-guided assembly platform based on the LACHESIS method [, ] with proprietary parameters developed at Phase Genomics as described by Peichel et al. [] (Fig. ). In brief, Proximo aligned the Hi-C PE reads to the SRA1 scaffolds, and the numbe […]

library_books

A streamlined tethered chromosome conformation capture protocol

2016
BMC Genomics
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 []. […]

library_books

Using linkage maps to correct and scaffold de novo genome assemblies: methods, challenges, and computational tools

2015
Front Genet
PMCID: 4473057
PMID: 26150829
DOI: 10.3389/fgene.2015.00220

[…] romatin interact generates a distribution indicative of the genomic distance between the loci and sufficient for ordering and orienting an assembled genome sequence (Kaplan and Dekker, ). The program LACHESIS (Burton et al., ) both constructs the frequency-based physical map and aligns scaffolds to the map. Hi-C requires a difficult molecular protocol (de Wit and de Laat, ) and has not been widely […]

library_books

Species Level Deconvolution of Metagenome Assemblies with Hi C–Based Contact Probability Maps

2014
PMCID: 4455782
PMID: 24855317
DOI: 10.1534/g3.114.011825

[…] omes (Figure S10). This suggests that in prokaryotic species, in sharp contrast with eukaryotic species, Hi-C is not very useful for ordering or orienting genomic content within chromosomes. However, Lachesis’ clustering algorithm can still be used to deconvolute chromosomes, including plasmids, inside prokaryotic cells. We applied this algorithm to the genome of Vibrio fischeri ES114, a bacterial […]

Citations

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

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