The ngscmd program depends on the zlib compression library.
To compile the ngscmd program:
./configure
followed by
make
The ngscmd program can work on a single fastQ input file, as well
as mate pair files. The fastQ files can be input into the ngscmd
program in either compressed or uncompressed form.
All seven commands of the ngscmd program are
| Command | Description |
|---|---|
| filter | remove low quality reads |
| trim | trim ends of reads |
| pair | align mated pairs in two fastQ files |
| score | convert Phred-scaled quality scores |
| rmdup | remove duplicate reads |
| kmer | count number of unique k-mers in fastQ file |
| join | join aligned mated pairs into single file |
Although their are many programs with functionality that is
similar to ngscmd, the motivation for developing this program
is that most tools exist in disparate form (save perhaps the fastx-toolkit)
and many exist only as high-level scripting languages, which
perform slowly. Thus, ngscmd was born out of my own frustration
trying to cobble together efficient computational tools for
processing short read data. The program is only beginning
development, so I would be happy to have others involved or
hear from people about what other functionality would be useful
for the program (or whether they have found bugs).