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Duplex-Process-Numbers.txt
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Duplex-Process-Numbers.txt
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start: 2n reads in n read pairs
tag_to_header:
progress numbers = read pairs (n = total)
input:
File Sequences Sequence Type Pairs
seq1.fq n reads unpaired
seq2.fq n reads unpaired
output:
File Sequences Sequence Type Pairs
seq1.fq.smi m reads unpaired
seq2.fq.smi m reads unapired
bwa aln: (x2)
progress numbers = read pairs (m = total)
input:
1:
File Sequences Sequence Type Pairs
seq1.fq.smi m reads unpaired
2:
File Sequences Sequence Type Pairs
seq2.fq.smi m reads unpaired
output:
1: seq1.aln
2: seq2.aln
bwa sampe:
progress numbers = read pairs (m = total)
input:
seq1.aln
seq2.aln
output:
File Sequences Sequence Type Pairs
PE.sam 2m reads m
samtools sort:
no progress numbers
input:
File Sequences Sequence Type Pairs
PE.sam 2m reads m
output:
File Sequences Sequence Type Pairs
PE.sort.bam 2m reads m
ConsensusMaker
progress numbers = reads (2m = total)
input:
File Sequences Sequence Type Pairs
PE.sort.bam 2m reads m
output:
File Sequences Sequence Type Pairs
SSCS.bam 2J SSCS J
SSCS_UP.bam j SSCS unpaired
SSCS_NM.bam ? reads unpaired
SSCS_LCC.bam ? reads unpaired
SSCS.tagcounts ---------Not a Sequence File--------
samtools sort:
no progress numbers
input:
File Sequences Sequence Type Pairs
SSCS.bam 2J SSCS J
output:
File Sequences Sequence Type Pairs
SSCS.sort.bam 2J SSCS J
DuplexMaker:
progress numbers = SSCS's (total = 2J)
input:
File Sequences Sequence Type Pairs
SSCS.sort.bam 2J SSCS J
output:
File Sequences Sequence Type Pairs
DCS.bam 2L DCS L
DCS_UP.bam l DCS unpaired
DCS.r1.fq L DCS unpaired
DCS.r2.fq L DCS unpaired
bwa aln: (x2)
progress numbers = DCS pairs (total = l)
input:
1:
File Sequences Sequence Type Pairs
DCS.r1.fq L DCS unpaired
2:
File Sequences Sequence Type Pairs
DCS.r2.fq L DCS unpaired
output:
1:
DCS.r1.aln
2:
DCS.r2.aln
bwa sampe:
progress numbers = DCS pairs (total = l)
input:
DCS.r1.aln
DCS.r2.aln
output:
File Sequences Sequence Type Pairs
DCS.sam 2L DCS L
samtools sort:
no progress numbers
input:
File Sequences Sequence Type Pairs
DCS.sam 2L DCS L
output:
File Sequences Sequence Type Pairs
DCS.aln.sort.bam 2L DCS L
n > m >> J > L
J > j, L > l
J = 2L + l