Genome-tools pipeline

Genome-tools specifications


Unique identifier OMICS_17123
Name Genome-tools
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A formatted sequence.
Input format FASTA
Output data A formatted sequence.
Output format FASTA
Operating system Unix/Linux, Mac OS, Windows
Programming languages Perl
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.23
Stability Stable
Maintained Yes



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  • person_outline Swaine Chen <>

Publication for Genome-tools

Genome-tools IN pipelines

PMCID: 5834201
PMID: 29462142
DOI: 10.1371/journal.pgen.1007233

[…] were adjusted to 5 nm in 10 mm tris-hcl ph 8.0 and sequenced with an illumina hiseq 2500., data analysis was performed in the wardrobe experiment management system ( [53]). for the analysis of h3k4me2, we used our publish data [42]. briefly, reads were aligned to the mouse genome (mm10) with bowtie (version 1.0.0 [54]) and displayed on a local […]

PMCID: 5537207
PMID: 28918033
DOI: 10.1016/j.omtn.2017.07.010

[…] used as the reference against the complete set of reads using bowtie 2.52 all non-aligned reads were filtered out by samtools.53 the resulting alignment data were converted to fasta format by ucsc genome tools.54 all mutants detected by pairwise alignment of each read from the fasta file against the reference target sequence were collected into an array suitable for further multiple […]

PMCID: 2851118
PMID: 20808525
DOI: 10.2174/138920210790218007

[…] been extended to include disease-marker association studies, genome annotation, alignment and assembly tools [3, 12]. currently, sequence simulation is an important method to test any of such new genome tools. this occurs because events as compositional bias, phylogenetic correlations, heterogeneous substitutions, indel rates, context-dependent mutation etc, change the information attached […]

Genome-tools institution(s)
Stanford University School of Medicine, Stanford, CA, USA
Genome-tools funding source(s)
This work was supported by Defence Advanced Research Projects Agency (DARPA) grant no. MDA972-00-1-0032, DOE grant no. DE-FG03- 01ER63219, and National Institutes of Health grant no. 2T32GM07365 to the Medical Scientist Training Program.

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