ARACHNE protocols

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ARACHNE specifications

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Unique identifier OMICS_01812
Name ARACHNE
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes

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Publications for ARACHNE

ARACHNE in pipelines

 (2)
2014
PMCID: 4161386
PMID: 25211235
DOI: 10.1371/journal.pone.0106704

[…] as follows: plasmid shotgun library was constructed from the three fosmid clones covering the repeat-induced over-collapsed region, and the resulting sanger pair-ended reads were assembled by using arachne . remaining gaps were joined using 454 reads extracted from the relevant region., protein-coding genes and trna genes were predicted by glimmer and trnascan-se , respectively. rrna genes […]

2012
PMCID: 3419625
PMID: 22554261
DOI: 10.1186/1756-0500-5-213

[…] two available gene predictions of the grapevine genome were produced from an 8x coverage assembly and from a 12x coverage assembly that included the genomic data from the 8x coverage version with arachne []. gaze software was used to perform the gene predictions for the 8x and the first version of the 12x (v0) prediction. the complete procedure is available in chapter 5 of the supplementary […]

ARACHNE in publications

 (55)
PMCID: 5634323
PMID: 28994819
DOI: 10.1038/sdata.2017.149

[…] assembly with at least 95% coverage and 95% identity., using the 24,535 transcripts from the jgi annotation that map to the falcon assembly, we updated the list of allelic pairs identified in the arachne assembly, using the custom script sd.find_allelic_pairs.py (github.com/paajanen/fc_scientific_data). out of the 6,071 allelic pairs identified in the arachne assembly 5,400 (89%) are found […]

PMCID: 5364385
PMID: 28322291
DOI: 10.1038/ncomms14742

[…] using sanger technology and paired-end reads were generated from 4 kb plasmid, 10 kb plasmid and 40 kb fosmid genomic clones. a total of 12.5 × sequence coverage was generated and assembled using arachne. a 175 kb scaffold corresponding to the mitochondrial genome was removed from this assembly for annotation and analysis. nearly all of the sequence is in large scaffolds; 98% of the sequence […]

PMCID: 5295586
PMID: 27913634
DOI: 10.1534/g3.116.032797

[…] using sanger technology: a 40 kb insert fosmid library (30,731 clones) and ∼100 kb insert bac library [15,000 clones (); table s1]. an initial assembly of flx and sanger data was generated with arachne (hybridassemble) (). the assembly was updated to incorporate the flx+ data by first generating a new de novo assembly of all data using newbler runassembly, with parameters –het and –large, […]

PMCID: 4932478
PMID: 27110816
DOI: 10.3390/pharmaceutics8020015

[…] their overlaps information is then constructed as a graph and (3) the consensus (c) sequence is finally inferred from the graph. software packages such as ssake, sharcgs, vcake, celera assembler, arachne, and pcap take the olc approach [,,,,,]., a de bruijn graph assembly is based on k-mer graphs from the input reads. the nodes of the graph are constituted with k-mers, the seed sequence […]

PMCID: 4729200
PMID: 26580012
DOI: 10.1038/nature16150

[…] along with mate-pairs, were generated at the okinawa institute of science and technology graduate university. more sequencing details are available in ., we assembled the saccoglossus genome with arachne, combined with bac/fosmid pair information to produce the final assembly. this saccoglossus assembly includes 7,282 total scaffold sequences spanning a total length of 758 mb. the relatively […]

ARACHNE institution(s)
Laboratory for Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA; Whitehead Institute/MIT Center for Genome Research, Cambridge, MA, USA; Department of Mathematics and Statistics, University of Nebraska, Lincoln, NE, USA; Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA

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