AMOS pipeline

AMOS specifications


Unique identifier OMICS_00008
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


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



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Additional information

Publications for AMOS

AMOS citations

PMCID: 4154752

[…] 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 […]

PMCID: 1088942

[…] 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.

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