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anfo - find best alignment of short reads to database


anfo [ option | file ... ]


anfo 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 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

-x num, --ixthreads num
Start 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 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 index files.

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