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PRICE specifications

Information


Unique identifier OMICS_01430
Name PRICE
Alternative name Paired-Read Iterative Contig Extension
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Complex metagenomic data
Input format fasta, fastq, priceq
Output format FASTA, priceq
Operating system Unix/Linux, Mac OS
Programming languages C++
Computer skills Advanced
Version 1.2
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline J. Graham Ruby

Publication for Paired-Read Iterative Contig Extension

PRICE citations

 (3)
library_books

Genome Sequencing of the Behavior Manipulating Virus LbFV Reveals a Possible New Virus Family

2016
Genome Biol Evol
PMCID: 5381508
PMID: 28173110
DOI: 10.1093/gbe/evw277

[…] values, including the k57 assembly, we choose to run another assembly without scaffolding with k = 57.To confirm the sequence of these contigs, we used the software Price (). This software performs a paired-read iterative contig extension and is designed to assemble sequences starting from a seed. Starting from 500 bp seeds defined in the middle of each viral contigs of the assembly k57 (without s […]

library_books

Metagenome Assembled Genome Sequence of Pseudomonas stutzeri Strain CO183 Isolated from a Coalbed Methane Well

2016
Genome Announc
PMCID: 5095482
PMID: 27811112
DOI: 10.1128/genomeA.01237-16

[…] cific marker genes in CheckM (), the resultant genome bin was 92.84% complete and had 13.64% contamination. The mapped Pseudomonas-assigned contigs and the raw metagenome reads were used as input for paired-read iterative contig extension (PRICE) (), and after 30 cycles the genome bin improved significantly, resulting in a bin of 117 contigs (4,522,918 bp) at 99.27% completeness and 0.4% contamina […]

library_books

Reconstruction of a Nearly Complete Pseudomonas Draft Genome Sequence from a Coalbed Methane Produced Water Metagenome

2016
Genome Announc
PMCID: 5054310
PMID: 27795237
DOI: 10.1128/genomeA.01024-16

[…] seudomonas genome bin using CLC genomics workbench (Qiagen) and mapped reads were reassembled with SPAdes (default parameters; contigs added as trusted contigs). The final contigs were extended using paired-read iterative contig extension (PRICE) ().The genome was 99.2% complete, with 0.75% contamination, and 0% strain heterogeneity using 833 marker genes specific to the genus Pseudomonas in Check […]

Citations

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PRICE institution(s)
Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA; GW Hooper Foundation Laboratories, University of California, San Francisco, CA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
PRICE funding source(s)
Funded by the Howard Hughes Medical Institute.

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