Provided by: jellyfish_1.1.2-1_amd64 bug

NAME

       jellyfish - count k-mers in DNA sequences

SYNOPSIS

       jellyfish  count  [-oprefix] [-mmerlength] [-tthreads] [-shashsize] [--both-strands] fasta
       [fasta ...  ]
       jellyfish merge hash1 hash2 ...
       jellyfish dump hash
       jellyfish stats hash
       jellyfish histo [-hhigh] [-llow] [-iincrement] hash
       jellyfish query hash

DESCRIPTION

       Jellyfish is a k-mer counter based on a multi-threaded hash table implementation.

       To count k-mers, use a command like:

       jellyfish count -m 22 -o output -c 3 -s 10000000 -t 32 input.fasta

       This will count the the 22-mers in species.fasta with 32 threads. The counter field in the
       hash  uses  only  3 bits and the hash has at least 10 million entries. Let the size of the
       table be s=2^l and the max reprobe value is less than 2^r, then the memory usage per entry
       in the hash is (in bits, not bytes) 2k-l+r+1.

       To  save  space,  the  hash table supports variable length counter, i.e. a k-mer occurring
       only a few times will use a small counter, a k-mer occurring many times will used multiple
       entries  in  the  hash. The -c specify the length of the small counter. The tradeoff is: a
       low value will save space per entry in the hash but will increase the  number  of  entries
       used, hence maybe requiring a larger hash. In practice, use a value for -c so that most of
       you k-mers require only 1 entry. For example, to count k-mers in a genome, where  most  of
       the  sequence  is  unique, use -c1 or -c2.  For sequencing reads, use a value for -c large
       enough to counts up to twice the coverage.

       When the orientation of the sequences in the input  fasta  file  is  not  known,  e.g.  in
       sequencing reads, using --both-strands (-C) makes the most sense.

       The following subcommand are used to look at the result: histo, dump, stats.

OPTIONS

   COUNT
       Count k-mers or qmers in fasta or fastq files

       Usage: jellyfish count [OPTIONS]... [file.f[aq]]...

       -h,--help
               Print help and exit

       --full-help
               Print help, including hidden options, and exit

       -V,--version
               Print version and exit

       -m,    --mer-len=INT
               Length of mer (mandatory)

       -s,    --size=LONG
               Hash size (mandatory)

       -t,    --threads=INT
               Number of threads (default=1)

       -o,    --output=STRING
               Output prefix (default=mer_counts)

       -c,    --counter-len=Length
               in bits Length of counting field (default=7)

       --out-counter-len=Length
               in bytes Length of counter field in output (default=4)

       -C,--both-strands
               Count both strand, canonical representation (default=off)

       -p,    --reprobes=INT
               Maximum number of reprobes (default=62)

       -r,--raw
               Write raw database (default=off)

       -q,--quake
               Quake compatibility mode (default=off)

       --quality-start=INT
               Starting ASCII for quality values (default=64)

       --min-quality=INT
               Minimum quality. A base with lesser quality becomes an N (default=0)

       -L,    --lower-count=LONG
               Don't output k-mer with count < lower-count

       -U,    --upper-count=LONG
               Don't output k-mer with count > upper-count

       --matrix=Matrix
               file Hash function binary matrix

       --timing=Timing
               file Print timing information

   HISTO
       Create an histogram of k-mer occurrences

       Usage: jellyfish histo [OPTIONS]... [database.jf]...

       --help
               Print help and exit

       -V,--version
               Print version and exit

       -s,    --buffer-size=Buffer
               length Length in bytes of input buffer (default=10000000)

       -l,    --low=LONG
               Low count value of histogram (default=1)

       -h,    --high=LONG
               High count value of histogram (default=10000)

       -i,    --increment=LONG
               Increment value for buckets (default=1)

       -t,    --threads=INT
               Number of threads (default=1)

       -o,    --output=STRING
               Output file (default=/dev/fd/1)

   DUMP
       Dump k-mer counts

       Usage: jellyfish stats [OPTIONS]... [database.jf]...

       -h,--help
               Print help and exit

       -V,--version
               Print version and exit

       -c,--column
               Column format (default=off)

       -t,--tab
               Tab separator (default=off)

       -L,    --lower-count=LONG
               Don't output k-mer with count < lower-count

       -U,    --upper-count=LONG
               Don't output k-mer with count > upper-count

       -o,    --output=STRING
               Output file (default=/dev/fd/1)

   STATS
       Statistics

       Usage: jellyfish stats [OPTIONS]... [database.jf]...

       -h,--help
               Print help and exit

       --full-help
               Print help, including hidden options, and exit

       -V,--version
               Print version and exit

       -L,    --lower-count=LONG
               Don't output k-mer with count < lower-count

       -U,    --upper-count=LONG
               Don't output k-mer with count > upper-count

       -v,--verbose
               Verbose (default=off)

       -o,    --output=STRING
               Output file (default=/dev/fd/1)

   MERGE
       Merge jellyfish databases

       Usage: jellyfish merge [OPTIONS]... [database.jf]...

       -h,--help
               Print help and exit

       -V,--version
               Print version and exit

       -s,    --buffer-size=Buffer
               length Length in bytes of input buffer (default=10000000)

       -o,    --output=STRING
               Output file (default=mer_counts_merged.jf)

       --out-counter-len=INT
               Length (in bytes) of counting field in output (default=4)

       --out-buffer-size=LONG
               Size of output buffer per thread (default=10000000)

       -v,--verbose
               Be verbose (default=off)

   CITE
       How to cite Jellyfish's paper

       Usage: jellyfish cite [OPTIONS]...

       -h,--help
               Print help and exit

       -V,--version
               Print version and exit

       -b,--bibtex
               Bibtex format (default=off)

       -o,    --output=STRING
               Output file (default=/dev/fd/1)

VERSION

       Version: 1.1 of 2010/10/1

BUGS

       *      jellyfish merge has not been parallelized and is very slow.

COPYRIGHT & LICENSE

       Copyright
              (C)2010,    Guillaume    Marcais    guillaume@marcais.net    and   Carl   Kingsford
              carlk@umiacs.umd.edu.

       License
              This program is free software: you can redistribute it and/or modify it  under  the
              terms  of  the  GNU  General  Public  License  as  published  by  the Free Software
              Foundation, either version 3 of the License, or (at your option) any later version.
              This program is distributed in the hope that it will be  useful,  but  WITHOUT  ANY
              WARRANTY;  without  even  the  implied warranty of MERCHANTABILITY or FITNESS FOR A
              PARTICULAR PURPOSE. See the GNU General Public License for more details.
              You should have received a copy of the GNU General Public License along  with  this
              program. If not, see <http://www.gnu.org/licenses/>.

AUTHORS

       Guillaume Marcais
       University of Maryland
       gmarcais@umd.edu

       Carl Kingsford
       University of Maryland
       carlk@umiacs.umd.edu