AMOS protocols

View AMOS computational protocol

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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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Additional information


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

Publications for AMOS

AMOS in pipelines

 (8)
2018
PMCID: 5798811
PMID: 29423233
DOI: 10.1038/s41438-017-0002-1

[…] produced with a total length of 702,204,081 bp, and the mean size was 567 bp. after checking quality by fastqc, we retained 235,005 contigs, and the longest length of a contig was 349,758 bp., the amos and minimus software with default parameters were used to assemble the chloroplast genome sequences of z. jujuba (shown in fig. ). the sequences and detail information of each contig were stored […]

2015
PMCID: 4428218
PMID: 26029184
DOI: 10.3389/fmicb.2015.00440

[…] pa13) were used as potential reference genomes. as the assemblies based on p. ananatis aj13355 resulted into highest coverage and mapping quality, this genome was used as reference genome for amoscmp. the result of quality and coverage control of the assembly of each p. ananatis genome sequence was calculated using qualimap v.1.0 (garcia-alcalde et al., ). in repetitive regions, […]

2014
PMCID: 4149021
PMID: 25197467
DOI: 10.4056/sigs.5541028

[…] for the phred/phrap/consed package []. in combination the assembly resulted in 39 contigs organized in four scaffolds. subsequently, small unlocalized contigs were mapped to the scaffolds using both minimus2 [] and nucmer []. by manual editing, the number of contigs could be reduced to 21, organized in one chromosomal scaffold. the remaining ordered gaps were closed by bridging pcr fragments […]

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

[…] to the reference genome with nucmer , , 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 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 […]

2013
PMCID: 3906814
PMID: 24030592
DOI: 10.1038/ismej.2013.153

[…] by metagenome reads tilling were selected as metagenomic islands (here after described as mgis) (). contigs from this study and previous dumpsite metagenome survey () were reassembled using minimus () at default parameter. we binned the metagenome contigs corresponding to reference genotypes (genus sphingobium) using tetranucleotide frequencies (correlation cutoff (r2)=0.9) and %gc […]


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AMOS in publications

 (137)
PMCID: 5905569
PMID: 29635365
DOI: 10.1093/gbe/evy074

[…] 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 […]

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

[…] 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 […]

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 […]

PMCID: 5788362
PMID: 29377955
DOI: 10.1371/journal.pone.0192003

[…] for each assembly, transcripts ≥80% sequence similarity were collapsed into clusters and the longest read retrieved using cd-hit-est []. the assemblies were then merged into a final assembly using minimus2 []. only contigs of ≥300 nt in length with average coverage ≥5 were included in the final assembly., microbial contamination was identified and removed from the e. varivestis transcriptome […]

PMCID: 5798811
PMID: 29423233
DOI: 10.1038/s41438-017-0002-1

[…] we report an innovative and efficient method for high-quality horticultural organellar genome assembly from next-generation sequencing (ngs) data. sequencing reads were first assembled by newbler, amos, and minimus software with default parameters. the remaining gaps were then filled through blastn search and pcr. the complete dna sequence was corrected based on illumina sequencing data using […]


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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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