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ANFO(1) - Linux manual page online | User commands

Find best alignment of short reads to database.

ANFO(1) User Manuals ANFO(1)


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 best. -x num, --ixthreads num Start num threads for indexing. Indexing normally uses less cpu power than align‐ ment, 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 Suppress all output except fatal errors. -v, --verbose Print a progress indicator during operation.


ANFO_PATH Colon separated list of directories searched for genome and index files.


/etc/popt The system wide configuration file for popt(3). anfo identifies itself as "anfo" to popt. ~/.popt Per user configuration file for popt(3). /usr/share/doc/anfo/example/*.cfg Example configuration files to be used with anfo.


None known.


Udo Stenzel <>

SEE ALSO anfo-tool(1), anfo-sge(1), fa2dna(1), dnaindex(1), popt(3), fasta(5)
Applications OCTOBER 2009 ANFO(1)
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anfo(1) referred by anfo-tool(1) | dnaindex(1) | fa2dna(1) | file-info(1)
refer to anfo-tool(1) | dnaindex(1) | fa2dna(1) | popt(3)
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