genomewalker
11/7/2019 - 7:14 AM

Repair paired fastq files

repair.md
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../opt/bbmap/repair.sh in=../DBs/fastq_clean/samples/tm3_1.2.gz out=r1.fq out2=r2.fq outs=sr.fq overwrite

Set INTERLEAVED to false
Started output stream.

Input:                          60113046 reads          4484553415 bases.
Result:                         60113046 reads (100.00%)        4484553415 bases (100.00%)
Pairs:                          1062720 reads (1.77%)   145407477 bases (3.24%)
Singletons:                     59050326 reads (98.23%)         4339145938 bases (96.76%)

Time:                           386.410 seconds.
Reads Processed:      60113k    155.57k reads/sec
Bases Processed:       4484m    11.61m bases/sec

../opt/bbmap/repair.sh in=../DBs/fastq_clean/samples/tm3_2.2.gz out=r1.fq out2=r2.fq outs=sr.fq overwrite

Set INTERLEAVED to false
Started output stream.

Input:                          21130570 reads          1603239364 bases.
Result:                         21130570 reads (100.00%)        1603239364 bases (100.00%)
Pairs:                          283668 reads (1.34%)    38155411 bases (2.38%)
Singletons:                     20846902 reads (98.66%)         1565083953 bases (97.62%)

Time:                           161.196 seconds.
Reads Processed:      21130k    131.09k reads/sec
Bases Processed:       1603m    9.95m bases/sec