MetAMOS protocols

View MetAMOS computational protocol

MetAMOS statistics

You need an account to access this content

info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Assembly chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

MetAMOS specifications

Information


Unique identifier OMICS_01426
Name MetAMOS
Software type Package/Module, Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C++, Java, Perl, Python
Computer skills Advanced
Version v1.5rc3
Stability Stable
Maintained Yes

Subtool


  • iMetAMOS

Download


Versioning


Add your version

Documentation


Maintainer


  • person_outline JIGSAW Team <>

Additional information


http://cbcb.umd.edu/software/metAMOS http://metamos.readthedocs.io/en/v1.5rc3/

Publications for MetAMOS

MetAMOS in pipelines

 (3)
2017
PMCID: 5687771
PMID: 29141051
DOI: 10.1371/journal.pone.0187832

[…] kit (sigma-aldrich, st. louis, mo, usa). dna libraries were prepared using nextera/nextera xt kits (illumina) followed by paired-end sequencing. contigs were assembled using spades [] through the imetamos extension [] of the metamos package []. the presence of resistance genes/mutations, carbapenemase genes and single nucleotide polymorphisms (snp) variations were determined using […]

2015
PMCID: 4533236
PMID: 26209388
DOI: 10.1016/j.jcv.2015.06.082

[…] were retained for downstream analyses. these sequences were mapped to a database containing a human genome and cdna references, to remove host sequences. unmapped sequences were entered into the metamos pipeline which employs multiple de novo assemblers with k-mer optimisation to assemble contigs. the contigs from the most effective assembly were then taxonomically classified using […]

2015
PMCID: 4550057
PMID: 26306392
DOI: 10.1186/s40168-015-0101-x

[…] assembly quality in complex metagenomes. the velvet assembler [] (veveth, hash size 45) was used to construct contigs. open reading frames (orf) were identified using metagenemark as implemented in metamos []. usearch (v5.2) [] was used to annotate orfs and unassembled reads with the kegg database (v54) []. e-value cutoffs of 1e−2 and 9e−46 were utilized for orfs and unassembled reads, […]

MetAMOS in publications

 (30)
PMCID: 5705806
PMID: 29202045
DOI: 10.1128/mSphere.00511-17

[…] reads were locally realigned using gatk v 2.8.1 (). we identified variants using pilon v 1.16 () (minimum read depth, 10; minimum mapping quality, 40; minimum base quality, 20)., we used the imetamos pipeline for de novo assembly (). we chose to compare assemblies from spades (), masurca (), and velvet (). kmergenie () was used to select kmer sizes for assembly. imetamos uses fastqc, […]

PMCID: 5687771
PMID: 29141051
DOI: 10.1371/journal.pone.0187832

[…] kit (sigma-aldrich, st. louis, mo, usa). dna libraries were prepared using nextera/nextera xt kits (illumina) followed by paired-end sequencing. contigs were assembled using spades [] through the imetamos extension [] of the metamos package []. the presence of resistance genes/mutations, carbapenemase genes and single nucleotide polymorphisms (snp) variations were determined using […]

PMCID: 5662582
PMID: 29123512
DOI: 10.3389/fmicb.2017.02088

[…] bray-curtis distances were performed with vegan. permutational anova (permanovas) was carried out with the ‘adonis’ function in vegan., for functional analysis, paired sequences were analyzed with metamos pipeline (). output files from functional annotation section in metamos, which consisted uniprot id of predicted proteins, were formatted with custom scripts to generate assigned uniprot id […]

PMCID: 5552977
PMID: 28798168
DOI: 10.1128/genomeA.00680-17

[…] randomly down-sampled to 100× using an estimated genome size of 5.3 mb, resulting in an average of 1.2 to 1.5 million paired-end reads per isolate. next, the down-sampled reads were assembled using imetamos () with idba_ud and spades (). idba_ud was selected as the best assembly for all six isolates. low confidence bases within the selected idba_ud () assemblies were masked out by mapping […]

PMCID: 5557581
PMID: 28771475
DOI: 10.1371/journal.pntd.0005693

[…] green monkey (chlorcebus sabeus) genome as a template. the remaining fastq files were additionally processed using trimmomatic to remove low quality sequence. finally, assembly was performed using imetamos [] using the standard parameters., nucleotide sequences were manually aligned with similar genbank sequences using muscle implemented in seaview []. untranslated regions (utrs) of alphavirus […]

MetAMOS institution(s)
National Biodefense Analysis and Countermeasures Center, Frederick, MD, USA

MetAMOS reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review MetAMOS