Table 1. Tools included as part of the ngs-preprocess pipeline (v2.6).

Software	Function	Source code	Version
sra-tools	Data download	github.com/ncbi/sra-tools	3.0.3
entrez-direct	Data download	ncbi.nlm.nih.gov/books/NBK179288/	16.2
fastp	Short-reads processing and reports	github.com/OpenGene/fastp	0.23.2
Porechop	Long-reads processing	github.com/rrwick/Porechop	0.2.4
PycoQC	Nanopore reads reports	github.com/a-slide/pycoQC	2.5.0.3
NanoPack	Long-reads quality control	github.com/wdecoster/nanopack	1.41.0
bam2fastx	Convert PacBio BAM to FASTq	github.com/PacificBiosciences/pbtk	3.1.0
bax2bam	Convert Legacy PacBio to BAM	anaconda.org/bioconda/bax2bam	0.0.9
lima	Demultiplex	github.com/PacificBiosciences/barcoding	2.7.1
ccs	Generate PacBio HiFi	ccs.how	6.4.0