GHOSTX statistics

info info

Citations per year

info

Popular tool citations

chevron_left Protein database search chevron_right
info

Tool usage distribution map

Tool usage distribution map
info info

Associated diseases

Associated diseases
Want to access the full stats & trends on this tool?

Protocols

GHOSTX specifications

Information


Unique identifier OMICS_08012
Name GHOSTX
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Some metagenome sequences produced from a DNA sequencer.
Input format FASTA
Output format GHOSTX outputs search results in the format similar to BLAST-tabular format.
Operating system Unix/Linux
Programming languages C++
Parallelization CUDA
License BSD 2-clause “Simplified” License
Computer skills Advanced
Version 1.3.7
Stability Stable
Requirements
gcc
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Yutaka Akiyama <>

Publications for GHOSTX

GHOSTX citations

 (11)
library_books

Flexible metagenome analysis using the MGX framework

2018
PMCID: 5937802
PMID: 29690922
DOI: 10.1186/s40168-018-0460-1

[…] method becomes available: blast [], for example, has been one of the most popular tools for database searches, despite its rather large computational overhead. recently developed alternatives like ghostx [] or diamond [] offer considerable acceleration compared to the original blast algorithm while retaining similar sensitivity. employing a workflow engine, these alternatives can effortlessly […]

library_books

A benzene degrading nitrate reducing microbial consortium displays aerobic and anaerobic benzene degradation pathways

2018
PMCID: 5852087
PMID: 29540736
DOI: 10.1038/s41598-018-22617-x

[…] v2.0.6 using default settings. bam files were converted with samtools v0.1.18, and gene coverage was calculated with subread version 1.4.6., the proteins were annotated with kaas, with sbh and ghostx as settings and with interproscan 5.6-48.0. the annotation was further enhanced by adding ec numbers via priam version march 06, 2013. further ec numbers were derived by text mining […]

library_books

Identification of fungi in shotgun metagenomics datasets

2018
PMCID: 5812651
PMID: 29444186
DOI: 10.1371/journal.pone.0192898

[…] fungal amplicon reads [–]., the second approach identifies species from shotgun metagenomes. most tools use custom-built databases, together with search algorithms such as blast, usearch and ublast, ghostx, and diamond [–]. these tools identify the database sequence most similar to a read from a metagenome. alternatively, algorithms such as kaiju and kraken assign reads to a lowest common […]

library_books

A Massively Parallel Sequence Similarity Search for Metagenomic Sequencing Data

2017
PMCID: 5666806
PMID: 29019934
DOI: 10.3390/ijms18102124

[…] similarity search sections at various scales, in which computational resources were efficiently used. the acceleration of ghost-mp compared with mpiblast should arise from the difference between the ghostx and blastx algorithms. furthermore, similar accelerations were observed in experiments with a compute node []., we further evaluated the scalability of ghost-mp on the k computer […]

library_books

Genomic insights into potential interdependencies in microbial hydrocarbon and nutrient cycling in hydrothermal sediments

2017
PMCID: 5569505
PMID: 28835260
DOI: 10.1186/s40168-017-0322-2

[…] [, ]. for the kaas- and cazy-based analysis, concatenated protein fasta sequences of each mag were uploaded to the kaas and dbcan webservers using the metagenome setting for kaas (parameters: ghostx, genes dataset, sbh assignment method) and default settings for dbcan., additionally, we searched for key metabolic genes using custom blast and hmmer databases using previously defined […]

library_books

Metaproteomics analysis of the functional insights into microbial communities of combined hydrogen and methane production by anaerobic fermentation from reed straw

2017
PMCID: 5560556
PMID: 28817657
DOI: 10.1371/journal.pone.0183158

[…] orthology and links annotation (koala) is kegg's internal annotation tool for k number assignment of kegg genes using ssearch computation. ghostkoala assign k numbers to the user's sequence data by ghostx searches, against a nonredundant set of kegg genes. thus, koala was used to annotate these metagenome sequences, which perform ko (kegg orthology) assignments from the proteins identification; […]


Want to access the full list of citations?
GHOSTX institution(s)
Department of Computer Science, School of Computing, Tokyo Institute of Technology, Tokyo, Japan; Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, Yokohama, Japan; Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, Tokyo, Japan
GHOSTX funding source(s)
Partly supported by the Strategic Programs for Innovative Research (SPIRE) Field 1 Supercomputational Life Science of the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan and Core Research for Evolutional Science and Technology (CREST) “Extreme Big Data” of the Japan Science and Technology Agency (JST).

GHOSTX reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review GHOSTX