AMOS protocols

AMOS specifications

Information


Unique identifier OMICS_00008
Name AMOS
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, C++, Perl
License Artistic License version 2.0
Computer skills Advanced
Stability Stable
Requirements QT
Maintained Yes

Subtools


  • AMOScmp
  • AMOScmp-shortReads
  • AMOScmp-shortReads-alignmentTrimmed
  • Amosvalidate
  • FRCurve
  • Minimus

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Versioning


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Additional information


http://amos.sourceforge.net/wiki/index.php/AMOS

Publications for AMOS

AMOS IN pipelines

 (4)
2014
PMCID: 4154752
PMID: 25188499
DOI: 10.1371/journal.pone.0106689

[…] the reference genome with nucmer [36], [37], we observed that the ends of several contigs overlapped with long stretches (1 kbp) of perfect sequence identity. we therefore used the assembly program minimus2 [38] to merge across these regions to generate supercontigs. all statistics in the following sections are based on this two-step assembly procedure combining celera and minimus2. the merging […]

2014
PMCID: 4154752
PMID: 25188499
DOI: 10.1371/journal.pone.0106689

[…] the assembly program minimus2 [38] to merge across these regions to generate supercontigs. all statistics in the following sections are based on this two-step assembly procedure combining celera and minimus2. the merging step resulted in the additional merging of 1,652 input contigs into 633 supercontigs, resulting in an improved assembly with a total of 5,598 contigs spanning a total of 147.4 […]

2012
PMCID: 3483213
PMID: 22577862
DOI: 10.1186/1471-2148-12-65

[…] another sequence (global outer fragments, gos)., the coverage of the new genomes was calculated by mapping each read to b. henselae houston-1 with nucmer (mummer 3.0 package) [66] and casm-layout (amos package) [23]. reads mapping to several regions (repeats) were randomly attributed. coverage was defined, for each base, as the number of reads covering that base. coverage was compared […]

2005
PMCID: 1088942
PMID: 15774024
DOI: 10.1186/gb-2005-6-3-r23

[…] genome assemblies, again using nucmer. we used the output of nucmer to extract from each genome the appropriate matching sequence, and we fed the results to the overlapper (hash-overlap) from the amos assembler [30] to generate all pairwise sequence alignments., all ankyrin repeat domain proteins identified by automated annotation were compiled and an alignment and tree were constructed using […]

AMOS institution(s)
Cold Spring Harbor, New York, NY, USA
AMOS funding source(s)
Supported, in part, by NIH grants R01-LM006845, R01-HG006677 and R01-HG004885 and by NSF grant IIS-0812111.

AMOS reviews

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