NAME

anfo - find best alignment of short reads to database

SYNOPSIS

anfo [ option | file ... ]

DESCRIPTION

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.

OPTIONS

-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 normally best.

--solexa-scale

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