3.1.1

pbtk container

Main tool: pbtk

Code repository: https://github.com/PacificBiosciences/pbtk

Basic information on how to use this tool:

• executables:
  • bam2fasta
  • bam2fastq
  • ccs-kinetics-bystrandify
  • extracthifi
  • pbindex
  • pbindexdump
  • pbmerge
  • zmwfilter
• help: -h, --help
• version: --version
• description: PacBio BAM toolkit

Full documentation: https://github.com/PacificBiosciences/pbtk

Example Usage

# bam2fasta
bam2fasta -o out in.bam
# bam2fastq
bam2fastq -o out in_1.bam in_2.bam in_3.xml in_4.bam
# ccs-kinetics-bystrandify
ccs-kinetics-bystrandify in.bam out.bam
# extracthifi
extracthifi in.bam out.bam
# pbindex
pbindex in.bam
# pbindexdump
pbindexdump in.bam.pbi > out.json
# pbmerge
pbmerge in1.bam in2.bam in3.bam > out.bam
# zmwfilter
zmwfilter --include 1,2,4,8,16 in.bam out.bam