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pbalign specifications


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
pbcore, blasr, pls2fasta, samFilter, samtoh5, loadPulses, virtualenv, numpy, h5py
Maintained Yes




No version available



  • person_outline Pacific Biosciences

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pbalign citations


Genomic Sequence of Saccharomyces cerevisiae BAW 6, a Yeast Strain Optimal for Brewing Barley Shochu

Genome Announc
PMCID: 5887032
PMID: 29622617
DOI: 10.1128/genomeA.00228-18

[…] m (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 v […]


“Targeted Sequencing by Gene Synteny,” a New Strategy for Polyploid Species: Sequencing and Physical Structure of a Complex Sugarcane Region

Front Plant Sci
PMCID: 5882829
PMID: 29643861
DOI: 10.3389/fpls.2018.00397

[…] ces for correction was set to 500 bp, and the number of partitions for consensus was set to 200. The contigs obtained with the assembler were subjected to error correction by remapping the reads with pbalign (v0.2). The PacBio reads were aligned using the BLASR algorithm (Chaisson and Tesler, ), and we performed assembly polishing with the Quiver tool (Chin et al., ). See Data Sheet topic “BAC as […]


A draft genome sequence for the Ixodes scapularis cell line, ISE6

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

[…] ength = 1000 bp, corMhapSensitivity = "low", and genomeSize = 1 Gbp. The contig consensus sequences were polished using SMRT Link version 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, the mapper […]


Resequencing of the Leishmania infantum (strain JPCM5) genome and de novo assembly into 36 contigs

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

[…] ally, 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 (http://bedtools.readthedocs.io/en/latest/content/tools/ […]


Genomics enabled analysis of the emergent disease cotton bacterial blight

PLoS Genet
PMCID: 5614658
PMID: 28910288
DOI: 10.1371/journal.pgen.1007003
call_split See protocol

[…] ti—min_idt 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 were ru […]


A high quality assembly of the Nile Tilapia (Oreochromis niloticus) genome reveals the structure of two sex determination regions

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

[…] rge and sort (with the ‘--deep’ flag) the pbalign.h5 output files for each SMRT cell. Finally, Quiver (GenomicConsensus version 0.9.2 and ConsensusCore version 0.8.8) was run on the merged and sorted pbalign output to produce an initial polished assembly.Pilon [] (version 1.18) was run on the intermediate Quiver-polished assembly produced above. Again, Bowtie2 (version 2.2.5 in ‘--very-sensitive’ […]

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