repair - toolkit for processing next-gen sequencing data
repair Version 2.0.4
- 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.
This manpage was written by Alexandre Mestiashvili for the Debian
distribution and
can be used for any other usage of the program.