library (ShortRead)
genome <- readDNAStrings(Fasta file)
sread(genome)[1]
quality(genome)[1]
##PhredQuality instance
pq <- PhredQuality (quality(fqsample))
# transform encoding into scores
qs <- as(pq, "IntegerList")
qs # Print score
qaSummary <- qa(fqsample, lane = 1)
#class : ShortReadQQA(1D)
#Names accessible with the quality assessment summary
names (qaSummary)