SYNOPSISanfo [ option | file ... ]
DESCRIPTIONanfo aligns (short) sequencing reads to a (gigabase sized) database. It uses a heuristic seeding method, but then applies a genuine aligner that allows gaps, understands damage patterns in ancient dna and produces an easy to interpret score.
Input files can be any variety of FastA or FastQ files, or a native anfo binary file, optinally compressed using gziporbzip2. The file format is automatically recognized and other formats may be added.
- -V, --version
Print version number and exit.
- -o file, --output file
Write output to
will be written in the native
binary format, which can be operated upon using
or the bindings to
- -c conffile, --config conffile
Read configuration from
This file configures which indices are used, and by extension to which
genomes an alignment is made, what parameters to use in the aligner and
can set paths. See the example file.
- -p num, --threads num
threads for alignment. One such thread per processor core is usually
- -x num, --ixthreads num
threads for indexing. Indexing normally uses less cpu power than
alignment, so fewer indexers than aligners is normally best.
When reading FastQ files, use the Solexa scale (log-odds-ratios) instead
of the standard Phread scale (probabilities). If you use
Solexa/Illumina sequencers, refer to your documentation whether you need
this. Else you don't.
- --fastq-origin ori
Set origin for FastQ decoding to
The standard and default is 33, but it must be set to 64 for some
versions of the Solexa/Illumina software. If you use Solexa/Illumina
sequencers, refer to your documentation whether you need this. Else you
- -q, --quiet
Suppress all output except fatal errors.
- -v, --verbose
Print a progress indicator during operation.
Colon separated list of directories searched for genome and index files.
- The system wide configuration file for popt(3). anfo identifies itself as "anfo" to popt.
- Per user configuration file for popt(3).
- Example configuration files to be used with anfo.
AUTHORUdo Stenzel <[email protected]>