Reading/parsing .ab1 sequencing files

Specific Domains Biology, Health, and Medicine
10

I was looking for the same a few months ago and came across the reader in BioSequences…

using BioSequences

# Sample .ab1 files at
# https://github.com/BioJulia/BioFmtSpecimens.git
# open a valid ab1 file
stream = open(ABIF.Reader, "BioFmtSpecimens/ABI/3730.ab1")

# all existing data tags
data = ABIF.get_tags(stream)

# Basecaller primary peaks
primary_peaks = stream["PBAS"]["PBAS2"]

# Base order array
bases = [base for base = stream["FWO_"]["FWO_"]]

# Dictionary of base trace values
channels = ["DATA9", "DATA10", "DATA11", "DATA12"]
trace_data = [stream["DATA"][channel] for channel = channels]
traces = Dict(zip(bases, trace_data))

# Basecaller peak quality scores
quality_scores = [Int(value) for value = stream["PCON"]["PCON2"]]
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