Awesome

gcpp takes an alignment in the form of a BAM file and polishes the references with the provided subreads from the alignment. It uses the Arrow algorithm in multi-molecule consensus setting and can reach up to QV60 at coverage 100. GCpp is the machine-code successor of the venerable GenomicConsensus suite which has reached EOL. Command-line parameters are the same as for GenomicConsensus, with the exception of not supporting Quiver/RSII anymore.

Availability

The latest gcpp can be installed via the bioconda package pbgcpp.

Please refer to our official pbbioconda page for information on Installation, Support, License, Copyright, and Disclaimer.

Latest Version

Version 2.0.2: Full changelog here

Execution

Input: Aligned subreads in PacBio BAM format (.bam).

Output: Polished contigs in .fasta or .fastq format.

FAQ

Why am I getting "Missing valid chemistry from input file, is this a proper PBBAM input file?"

You have likely aligned a FASTQ/FASTA file or a BAM file that yielded an invalid PBBAM file. A PBBAM file is a BAM with additional metadata. You cannot, in general, align FASTQ files and produce valid PBBAMs. We recommend you align the .subreads.bam or .subreadset.xml file using pbmm2 which produces valid PBBAMs.

Licenses

PacBio® tool gcpp, distributed via Bioconda, is licensed under BSD-3-Clause-Clear

Changelog

• 2.0.2:
  • Require FAI index upfront when passing the -w argument. This would lead to rare crashes when users did not have FAI files present.
• 2.0.1:
  • Fixed a buffer overflow in Arrow that could lead to segfaults in rare cases.
• 2.0.0:
  • SMRT Link v10.0 release candidate
• 1.0.0:
  • SMRT Link v8.0 release candidate
  • Only perform QV computation when required (.fasta-only output will skip QV computation)
  • Allow 0-byte input references
  • Logs limited to at most 1000 lines per contig
  • Improved UX for invalid BAM inputs
  • Do not require PB Index, only BAI
• 0.0.1
  • Released with SMRT Link v7.0
  • First commercial release

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