repair(1)
toolkit for processing next-gen sequencing data
Description
REPAIR
NAME
repair - toolkit for processing next-gen sequencing data
DESCRIPTION
repair Version 2.0.1
Find reads that are from the same pair in the input and then place them next
to each other in the output. A dummy read is added for each singleton read that does not have a pair. The output file is compatible with featureCounts program.
Usage:
./repair [options] -i <input_file> -o <output_file>
Required
arguments:
-i <string>
Name of input file. BAM format by default.
-o <string>
Name of output file. The output file is in BAM format.
Optional arguments:
|
-S |
The input file is in SAM format. | ||
|
-c |
Compress the output BAM file. This will reduce the size of BAM file, but will increase the time of retrieving reads from BAM file. |
-T <int>
Number of CPU threads. 8 by default.
|
-d |
Do not add dummy reads for singleton reads. | ||
|
-t |
Do not include sequences and quality scores of reads in the output file. |
AUTHOR
This manpage was
written by Nilesh Patra for the Debian distribution and
can be used for any other usage of the program.