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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
Maintained Yes


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




No version available

Additional information

Publications for AMOS

AMOS citations


Complete Genome Sequences of Seven Vibrio anguillarum Strains as Derived from PacBio Sequencing

Genome Biol Evol
PMCID: 5905569
PMID: 29635365
DOI: 10.1093/gbe/evy074
call_split See protocol

[…] ic Biosciences RS II instrument using P6-C4 chemistry with 360-min movie time. Reads were assembled using HGAP v3 (Pacific Biosciences, SMRT Analysis Software v2.3.0). Contigs were circularized using Minimus2 software of Amos package ().For CNEVA NB11008 and JLL237, the number of circular contigs were bioinformatically corrected. The BRIG software () was used to compare the 11 complete genomes (wi […]


A new strategy to infer circularity applied to four new complete frog mitogenomes

Ecol Evol
PMCID: 5916287
PMID: 29721275
DOI: 10.1002/ece3.3918

[…] gy searches using BLAST (Altschul, Gish, Miller, Myers, & Lipman, ) and comparing the size of the assembled genome to the reference (Soorni, Haak, Zaitlin, & Bombarely, ). Additionally, tools such as Minimus2 (Sommer, Delcher, Salzberg, & Pop, ) and Circlator (Hunt et al., ) perform circularization of genome assemblies by joining individual contigs, although they do not clip circular fragments inc […]


In Vitro Culture of the Insect Endosymbiont Spiroplasma poulsonii Highlights Bacterial Genes Involved in Host Symbiont Interaction

PMCID: 5874924
PMID: 29559567
DOI: 10.1128/mBio.00024-18
call_split See protocol

[…] CA, USA) in a 240-min movie. Assembly was performed with HGAP (hierarchical genome assembly process) version 2 from the PacBio smrtpipe (v2.3.0). Circularization of main contig 1 was performed using Amos (v3.1.0; Amos Consortium; Plasmid contig 7 was refined using the PacBio read data from Paredes et al. () with Quiver version 1. Genome annotation was performed with […]


Analyzing AbrB Knockout Effects through Genome and Transcriptome Sequencing of Bacillus licheniformis DW2

Front Microbiol
PMCID: 5863516
PMID: 29599755
DOI: 10.3389/fmicb.2018.00307

[…] . The polymerase reads were assembled de novo with Hierarchical Genome Assembly Process 3 (HGAP3) within the SMRT Analysis version 2.3.0 software (). Subsequently, the best assembly was selected, and Minimus 2 was used for trimming the circular contig (). The replication origin was determined by aligning the DW2 genomic sequence with B. licheniformis DSM13.For identification of methylated bases an […]


Resequencing of the Leishmania infantum (strain JPCM5) genome and de novo assembly into 36 contigs

Sci Rep
PMCID: 5741766
PMID: 29273719
DOI: 10.1038/s41598-017-18374-y

[…] ccuracy of these and the rest of assemblies was monitored by alignment of sequencing reads and its visualization by IGV. Contigs belonging to the chromosomes 12, 15, 22, 26 and 28, were joined by the minimus2 assembler, which uses an algorithm that calculates overlaps between contigs. On the other hand, the two contigs forming the chromosome 33 could be joined by means of the SSPACE-LongRead tool, […]


Genomic features of “Candidatus Venteria ishoeyi”, a new sulfur oxidizing macrobacterium from the Humboldt Sulfuretum off Chile

PLoS One
PMCID: 5728499
PMID: 29236755
DOI: 10.1371/journal.pone.0188371

[…] etect C- and KS- domains, were used. Additionally, the identification of CRISPR repeats was carried out by the CRISPRFinder tool []. The assembly visualization was made with the Hawkeye tool from the AMOS open-source project Version 3.1.0 [] and Artemis []. The circular representation of the draft genome was built through the Circos software []. Finally, CDSs were considered as protein-coding gene […]


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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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