Provided by: anfo_0.98-9_amd64 bug


       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.


              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.


       None known.


       Udo Stenzel <>


       anfo-tool(1), anfo-sge(1), fa2dna(1), dnaindex(1), popt(3), fasta(5)