Convert .bam to .fastq and remove reads with remnant PacBio adapter sequences

Dependencies:

• BamTools
• BLAST+

Optional:

• pigz

Add script and database to your path using:

export PATH=$PATH:[PATH TO HiFiAdapterFilt]
export PATH=$PATH:[PATH TO HiFiAdapterFilt]/DB

bash pbadapterfilt.sh [ -p file Prefix ] [ -l minimum Length of adapter match to remove. Default=44 ] [ -m minimum percent Match of adapter to remove. Default=97 ] [ -t Number of threads for blastn. Default=8 ] [ -o outdirectory prefix Default=. ]

All flags are optional.

If no -p argument is provided, the script will run on all sequence files (.bam, .fastq, .fastq.gz, .fq, .fq.gz) in the working directory.

• {prefix}.contaminant.blastout (Output of BLAST search)
• {prefix}.blocklist (Headers of PB adapter contaminated reads to be removed)
• {prefix}.filt.fastq.gz (Fastq reads free of PB adapter sequence ready for assembly)
• {prefix}.stats (File with simple math on number of reads removed, etc)

If this script is useful to you, please cite the following in your publication:

@article{HiFiAdapterFilt,
   author = {Sim, Sheina B. and Corpuz, Renee L. and Simmonds, Tyler J. and Geib, Scott M.},
   title = {HiFiAdapterFilt, a memory efficient read processing pipeline, prevents occurrence of adapter sequence in PacBio HiFi reads and their negative impacts on genome assembly},
   journal = {BMC Genomics},
   volume = {23},
   number = {1},
   pages = {157},
   ISSN = {1471-2164},
   DOI = {10.1186/s12864-022-08375-1},
   url = {https://doi.org/10.1186/s12864-022-08375-1},
   year = {2022},
   type = {Journal Article}
}

Sheina B. Sim
USDA-ARS
US Pacific Basin Agricultural Research Service
Hilo, Hawaii, 96720 USA
[email protected]

This script is in the public domain in the United States per 17 U.S.C. § 105