Commit bc0b620d authored by Denis Jacob Machado's avatar Denis Jacob Machado

Update awa-bootstrap.py

parent 317739b4
......@@ -6,6 +6,9 @@
# Given a reference sequence in FASTA format and short sequence reads in FASTA
# format, check if there is evidence for circularity.
# The second program of two, awa-bootstrap maps reads (in fastq format) against the
# putative circular sequence (fragment in fasta format) found by awa-trim.py.
# Phred score: # Sanger format can encode a Phred quality score from 0 to 93 using ASCII
# 33 to 126. Illumina's newest version (1.8) of their pipeline CASAVA will directly
# produce fastq in Sanger format.
......@@ -27,7 +30,7 @@ parser=argparse.ArgumentParser()
# Required
parser.add_argument("-i","--index",help="Index name (Bowtie2 >= v.2.3.1)",type=str,required=True)
parser.add_argument("-f","--fragment",help="Consensus sequence in FASTA format",type=str,required=True)
parser.add_argument("-r","--reads",help="Interleaves paired-end reads in FASTQ format (CASAVA +1.8)",type=str,required=True)
parser.add_argument("-r","--reads",help="Interleaved paired-end reads in FASTQ format (CASAVA +1.8)",type=str,required=True)
parser.add_argument("-s","--sam",help="Alignment in SAM format (Bowtie2 >= v.2.3.1)",type=str,required=True)
# Not required (have default values)
......
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