anfo - find best alignment of short reads to database
anfo [ option | file ... ]
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 gzip
. 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 file. file will be written in
the native anfo binary format, which can be operated upon using
anfo-tool or the bindings to guile.
- -c conffile, --config conffile
- Read configuration from conffile. 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
- Start num threads for alignment. One such thread per
processor core is usually best.
- -x num, --ixthreads num
- Start num threads for indexing. Indexing normally
uses less cpu power than alignment, so fewer indexers than aligners is
- 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 ori. 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 don't.
- -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
The system wide configuration file for
popt(3). anfo identifies itself as "anfo" to
Per user configuration file for
Example configuration files to be used with
Udo Stenzel <email@example.com>