ARACHNE protocols

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ARACHNE specifications


Unique identifier OMICS_01812
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

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 […]

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

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 ( 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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