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Yuan Li edited this page Jan 16, 2017 · 17 revisions

Welcome to the pbalign wiki!

ATTENTION: pbalign and blasr has been significantly changed in SMRTAnalysis v3.0. And blasr and pbalign in SMRTAnalysis v3.0 (and later version) are NOT BACKWARD-COMPATIBLE with legacy blasr and pbalign in SMRTAnalysis v2.3 (and previous version).

PacBio SEQUEL sequencing data are now saved in BAM files and represented by DATASETS. We recommend to use SMRTAnalysis v3.0+ (e.g., the latest blasr and pbalign in GitHub) to align SEQUEL sequencing data.

PacBio RSII sequencing data used to be saved in BAX/BAS.H5 files. Although users can still use SMRTAnalysis v2.3- for analyzing RSII sequencing data, we recommend to first convert BAX/BAS.H5 files to BAM files and then analyze BAM files using SMRTAnalysis v3.0+ (e.g., the latest blasr and pbalign in GitHub)

Release:

  • pbalign v0.3.0 no longer supports CMP.H5 output, and must go with blasr v5.1+.

  • pbalign v0.2.0 replaced pbalign.py by pbalign.

Tutorials: