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pbalign specifications

Information


Unique identifier OMICS_18565
Name pbalign
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTA,Base HDF5,Pulse HDF5,Circular Consensus Sequence (CCS) HDF5, file or file names (FOFN)
Output format SAM,Compare HDF5
Programming languages Perl, Python, Shell (Bash)
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Stability Stable
Requirements
pbcore, blasr, pls2fasta, samFilter, samtoh5, loadPulses, virtualenv, numpy, h5py
Maintained Yes

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Versioning


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Documentation


Maintainer


  • person_outline Pacific Biosciences <>

Additional information


https://github.com/PacificBiosciences/pbalign/wiki

pbalign in publications

 (8)
PMCID: 5887032
PMID: 29622617
DOI: 10.1128/genomeA.00228-18

[…] (illumina). the reads from both platforms were combined to obtain a final genome sequence. pacbio read sequences were assembled with canu version 1.5. the original reads were mapped to contigs with pbalign version 0.3.1, and errors were corrected using genomicconsensus version 2.1. miseq reads were mapped using burrows-wheeler aligner (bwa) version 0.7.12, and errors were corrected using pilon […]

PMCID: 5883391
PMID: 29707202
DOI: 10.5256/f1000research.14813.r31696

[…] = 1000 bp, cormhapsensitivity = "low", and genomesize = 1 gbp. the contig consensus sequences were polished using smrt link version 5.0.1.9585 which includes arrow version 2.2.1, blasr 5.3, and pbalign 0.3.1 (pacific biosciences)., short reads were mapped with bowtie2 ( ) version 2.2.5 using either end-to-end or local-alignment mode as indicated in the text. using default settings, […]

PMCID: 5741766
PMID: 29273719
DOI: 10.1038/s41598-017-18374-y

[…] a coverage analysis on the newly assembled chromosomes was performed using both illumina and pacbio reads. illumina reads were aligned by bowtie2 (ref.), and pacbio bax.h5 reads were aligned by pbalign (which uses the blasr method). coverage analysis was done from each alignment along the 36 chromosomes using the genomecoveragebed tool […]

PMCID: 5614658
PMID: 28910288
DOI: 10.1371/journal.pgen.1007003

[…] 0.72—min_cov 4—local_match_count_threshold 2—max_n_read 320—n_core 6; overlap_filtering_setting = —max_diff 90—max_cov 300—min_cov 10—bestn 10. assemblies were polished using iterations of pbalign and quiver, which can be found at https://github.com/pacificbiosciences/pbalign/commit/cda7abb and https://github.com/pacificbiosciences/genomicconsensus/commit/43775fa. two iterations […]

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

[…] [] (version 2.3.0.140936) was used for polishing the 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. […]


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