famas - FastQ massaging

Yet another program for FastQ massaging:

Features:

• Quality- and length-based trimming
• Random sampling
• Splitting into multiple files
• Built-in order checking for paired-end files
• Built-in checks for valid quality ranges
• Gzip support

Installation

Famas depends on libz, argtable3 and Heng Li's kseq. The latter two come with the famas source and libz is very likely already installed on your system.

Go the dist directory and download the latest tarball.

Unpack the source and do the GNU triple jump:

./configure
make
make install

If configure complains about missing libraries of which you are sure they are installed, just in an unusual directory, modify your CFLAGS and LDFLAGS environment variables accordingly. For example, if you have libz installed via Macports which resides in /opt/local you might want to use:

./configure CFLAGS='-I/opt/local/include'  LDFLAGS='-L/opt/local/lib'

Note, if you use the github source or github releases (and not the distribution tarball in the distribution directory), you might have to run the following once to update the autotools files (configure and Makefile.in):

autoreconf
automake --add-missing

and possibly

[g]libtoolize
autoreconf

Usage

famas -h will produce the following help:

famas (0.0.12) - yet another program for FAstq MASsaging

Usage: famas [-fah] -i <file> [-j <file>] -o <file> [-p <file>] [-m <int>] [-5 <int>] [-3 <int>] [-l <int>] [-e <33|64>] [-s <int>] [-x <int>] [--quiet] [--debug]

Files:
  -i, --in1=<file>          Input FastQ file (gzip supported; '-' for stdin)
  -j, --in2=<file>          Other input FastQ file if paired-end (gzip supported)
  -o, --out1=<file>         Output FastQ file (will be gzipped; '-' for stdout)
  -p, --out2=<file>         Other output FastQ file if paired-end input (will be gzipped)

Trimming & Filtering:
  -m, --minbq50p=<int>      Discard reads if >50% of bases have a BQ less or equal than this number. Applied before other BQ filters. Default: 0
  -5, --min5pqual=<int>     Trim from start/5'-end if base-call quality is below this value. Default: 0
  -3, --min3pqual=<int>     Trim from end/3'-end if base-call quality is below this value (Illumina guidelines recommend 3). Default: 0
  -l, --minlen=<int>        Discard read (pair) if (either) read length after trimming is below this length. Default: 0
  -e, --phred=<33|64>       Qualities are ASCII-encoded Phred +33 (e.g. Sanger, SRA, Illumina 1.8+) or +64 (e.g. Illumina 1.3-1.7). Default: 33

Sampling:
  -s, --sampling=<int>      Randomly sample roughly every <int>th read (after filtering, if used)
  -x, --split-every=<int>   Split every x reads. Requires XXXXXX in output names, which will be replaced with split number

Misc:
  -f, --overwrite           Overwrite output files
  -a, --append              Append to output files
  -h, --help                Print this help and exit
  --quiet                   No output, except errors
  --debug                   Print debugging info