The umgap uniq command can be used to join together the predictions of 2 paired ends before aggregation.

Usage

The input is given in a FASTA format on standard input. The content of all consecutive records with the same FASTA header is joined under a single header, separated by newlines (or another separated set with -s).

A delimiter can be passed with the -d option to drop this delimiter and everything after it from the FASTA header before comparing it.

$ cat input.fa
>header1/1
147206
240495
>header1/2
1883
1
1883
1883
$ umgap uniq -d / < input.fa
>header1
147206
240495
1883
1
1883
1883
-h / --help
Prints help information
-V / --version
Prints version information
-w / --wrap
Wrap the output sequences
-s / --separator s
Separator between output items [default: newline]
-d / --delimiter d
Strip FASTA headers after this string