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pbh5tools specifications

Information


Unique identifier OMICS_05138
Name pbh5tools
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format H5
Biological technology Pacific Biosciences
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Subtools


  • bash5tools
  • cmph5tools

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Documentation


pbh5tools in publications

 (4)
PMCID: 5850651
PMID: 28957512
DOI: 10.1093/molbev/msx212

[…] and evaluated with several tools in smrt analysis (v2.2.0 and v2.3.0) and in-house pipelines (, online). briefly, the raw reads in fastq format were extracted from h5 format by bash5tool in the pbh5tools packages. the suggested parameters (minreadscore = 0.75, minsrl = 50, minrl = 50) were adopted to filter and trim the raw reads. the circular consensus module in consensustools […]

PMCID: 5414186
PMID: 28464822
DOI: 10.1186/s12864-017-3723-5

[…] canu #14 assembly using the 44x raw pacbio reads. first, each smrt cell was separately aligned to the unpolished canu assembly using pbalign (version 0.2.0.138342) with the ‘--forquiver’ flag. next, cmph5tools.py (version 0.8.0) was used to merge and sort (with the ‘--deep’ flag) the pbalign.h5 output files for each smrt cell. finally, quiver (genomicconsensus version 0.9.2 and consensuscore […]

PMCID: 4889671
PMID: 27172212
DOI: 10.1534/g3.116.029389

[…] sequencing kit (pacific biosciences) to 155 × depth of coverage with an extracted subread length of 2881 ± 2177 bp and maximum read length of 35,845 bp (using –minreadscore 0.75,–minlength 500 for pbh5tools, pacific biosciences, menlo park, ca), and by using the illumina hiseq technology with 100 bp paired-end reads with a raw depth of coverage of 1038 ×. an optimal assembly method was found […]

PMCID: 4787755
PMID: 26101252
DOI: 10.1093/nar/gkv630

[…] smrt sequencing was performed on the pacbio rsii, using 2-h movies., generation of initial data set a fasta file containing the initial set of reads to be analyzed is generated with the bash5tools.py code (smrt analysis v2.2.0 for ubuntu 10.04), which uses information generated by the pacbio instrument contained in the bas.h5 and bax.h5 files. only reads longer than 2 kb […]


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