AMOS statistics

info info

Citations per year

Number of citations per year for the bioinformatics software tool AMOS
info

Tool usage distribution map

This map represents all the scientific publications referring to AMOS per scientific context
info info

Associated diseases

This word cloud represents AMOS usage per disease context
info

Popular tool citations

chevron_left Genome assembly Assembly reconciliation Reference-assisted assembly chevron_right
Want to access the full stats & trends on this tool?

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

Download


galaxy.png
conda.png

Versioning


No version available

Additional information


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

Publications for AMOS

AMOS citations

 (113)
call_split

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

2018
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 […]

library_books

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

2018
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 […]

call_split

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

2018
MBio
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; http://amos.sourceforge.net). Plasmid contig 7 was refined using the PacBio read data from Paredes et al. () with Quiver version 1. Genome annotation was performed with […]

library_books

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

2018
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 […]

library_books

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

2017
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, […]

library_books

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

2017
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 […]


Want to access the full list of citations?
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

star_border star_border star_border star_border star_border
star star star star star

Be the first to review AMOS