[Container Request]: PacBio Secondary Analysis Tools

[Kincekara]

What tool are you looking for and why?

PacBio installs all the tools with its SmartLink software as a bundle. However, they may be useful as individual containers for potential independent analysis of PacBio data, and cloud-native pipelines.
Tools are listed here: https://github.com/PacificBiosciences/pbbioconda

I will try to dockerize those tools as much as possible.

Package	Linux	Mac	Description
isoseq	Y	-	Scalable de novo isoform discovery (Release Notes)
jasmine	Y	-	Predict 5mC in PacBio HiFi reads (Release Notes)
lima	Y	-	Demultiplex barcoded samples (Release Notes)
pbaa	Y	Y	HiFi specific Amplicon Analysis
pbbam	Y	Y	BAM C++ library, tools are now in pbtk (Release Notes)
pbccs	Y	-	Generate HiFi reads for Sequel II (Release Notes)
pbcommand	Y	Y	Common models, CLI tool contract and SMRT Link service interface
pbcopper	Y	Y	Core C++ library for data structures, algorithms, and utilities (Release Notes)
pbcore	Y	Y	Python library for reading and writing data files
pbcoretools	Y	Y	CLI tools and add-ons for PacBio's core APIs (incl dataset)
pbfusion	Y	-	A fusion gene detection tool for all Iso-Seq data types (Release Notes)
pbipa	Y	-	Construct very contiguous, high quality de novo genome assemblies using the IPA HiFi assembler. (Release Notes)
pbmarkdup	Y	-	Mark duplicate reads from PacBio sequencing of an amplified library (Release Notes)
pbmm2	Y	-	A minimap2 frontend for PacBio native data formats (Release Notes)
pbpigeon	Y	-	PacBio transcript toolkit (Release Notes)
pbskera	Y	-	Read deconcatination (Release Notes)
pbsv	Y	-	Structural variant analysis (Release Notes)
pbtk	Y	-	PacBio BAM toolkit contains bam2fasta, bam2fastq, ccs-kinetics-bystrandify, extracthifi, pbindex, pbindexdump, pbmerge, zmwfilter (Release Notes)
recalladapters	Y	-	Recall adapters (Release Notes)
trgt	Y	-	Tandem repeat genotyping and visualization (Release Notes)