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Real-world example

This is an example of an end-to-end cmd-line-only workflow:

# Download HiFi reads
$ wget https://downloads.pacbcloud.com/public/dataset/ISMB_workshop/singlecell/ccs.bam

# Download primers
$ wget https://downloads.pacbcloud.com/public/dataset/ISMB_workshop/singlecell/primers.fasta

# Check lima version to be >= 2.0.0
$ lima --version
lima 2.0.0 (commit v2.0.0)

# Check isoseq3 version to be >= 3.4.0
$ isoseq3 --version
isoseq3 3.4.0 (commit v3.4.0)

# Primer removal
$ lima --isoseq ccs.bam primers.fasta output.bam

# Clip UMI and cell barcode
$ isoseq3 tag output.5p--3p.bam flt.bam --design T-8U-12B

# Remove poly(A) tails and concatemer
$ isoseq3 refine flt.bam primers.fasta fltnc.bam --require-polya

# Deduplicate transcripts from the identical molecule
$ isoseq3 dedup fltnc.bam dedup.bam --log-level INFO

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