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NAME

       jellyfish - software to 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
       jellyfish cite

       Plus equivalent version for Quake mode: qhisto, qdump and qmerge.

DESCRIPTION

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

   COUNTING AND MERGING
       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 input.fasta with 32 threads. The counter field  in  the
       hash uses only 3 bits and the hash has at least 10 million entries.

       The  output files will be named output_0, output_1, etc. (the prefix is specified with the
       -o switch). If the hash is large enough (has specified by the -s switch) to  fit  all  the
       k-mers,  there  will  be only one output file named output_0. If the hash filled up before
       all the mers were read, the hash is dumped  to  disk,  zeroed  out  and  reading  in  mers
       resumes.  Multiple  intermediary  files  will  be  present  on  the disks, named output_0,
       output_1, etc.

       To obtain correct results from the other sub-commands (such as histo,  stats,  etc.),  the
       multiple  output  files,  if  any,  need to be merged into one with the merge command. For
       example with the following command:

       jellyfish merge -o output.jf output\_*

       Should you get many intermediary output files (say hundreds), the size of the  hash  table
       is  too  small. Rerunning Jellyfish with a larger size (option -s) is probably faster than
       merging all the intermediary files.

   ORIENTATION
       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.

       For  any  k-mer  m,  its  canonical  representation is m itself or its reverse-complement,
       whichever  comes  first  lexicographically.  With  the  option  -C,  only  the   canonical
       representation  of  the  mers  are stored in the hash and the count value is the number of
       occurrences of both the mer and its reverse-complement.

   CHOOSING THE HASH SIZE
       To achieve the best performance, a minimum number of intermediary files should be  written
       to  disk.  So the parameter -s should be chosen to fit as many k-mers as possible (ideally
       all of them) while still fitting in memory.

       We consider to examples: counting mers in sequencing reads and in a finished genome.

       First, suppose we count k-mers in short sequencing reads: there are n reads and  there  is
       an  average  of  1 error per reads where each error generates k unique mers. If the genome
       size is G, the size of the hash (option -s) to fit all k-mers at once is estimated to: $(G
       +  k*n)/0.8$. The division by 0.8 compensates for the maximum usage of approximately $80%$
       of the hash table.

       On the other hand, when counting k-mers in an assembled sequence of length G,  setting  -s
       to G is appropriate.

       As  a  matter of convenience, Jellyfish understands ISO suffixes for the size of the hash.
       Hence '-s 10M' stands 10 million entries while '-s 50G' stands for 50 billion entries.

       The actual memory usage of the hash table can be computed as follow. The  actual  size  of
       the  hash  will  be rounded up to the next power of 2: s=2^l. The parameter r is such that
       the maximum reprobe value (-p) plus one is less than 2^r. Then the memory usage per  entry
       in  the hash is (in bits, not bytes) 2k-l+r+1. The total memory usage of the hash table in
       bytes is: 2^l*(2k-l+r+1)/8.

   CHOOSING THE COUNTING FIELD SIZE
       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.

       Important: the size of the couting field does NOT change the result, it only  impacts  the
       amount  of  memory used. In particular, there is no maximum value in the hash. Even if the
       counting field uses 5 bits, a k-mer occurring 2 million times will have a  value  reported
       of 2 million (i.e., it is not capped at 2^5).

       The  -c specify the length (in bits) of the counting field. The trade off is as follows: a
       low value will save space per entry in the hash but can potentially 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. For example, if the coverage is 10X, choose a counter length of 5 (-c5) as  $2^5
       > 20$.

SUBCOMMANDS AND OPTIONS

   COUNT
       Usage: jellyfish count [options] file:path+

       Count k-mers or qmers in fasta or fastq files

       Options (default value in (), *required):

       -m,    --mer-len=uint32
               *Length of mer

       -s,    --size=uint64
               *Hash size

       -t,    --threads=uint32
               Number of threads (1)

       -o,    --output=string
               Output prefix (mer_counts)

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

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

       -C,--both-strands
               Count both strand, canonical representation (false)

       -p,    --reprobes=uint32
               Maximum number of reprobes (62)

       -r,--raw
               Write raw database (false)

       -q,--quake
               Quake compatibility mode (false)

       --quality-start=uint32
               Starting ASCII for quality values (64)

       --min-quality=uint32
               Minimum quality. A base with lesser quality becomes an N (0)

       -L,    --lower-count=uint64
               Don't output k-mer with count < lower-count

       -U,    --upper-count=uint64
               Don't output k-mer with count > upper-count

       --matrix=Matrix
               file Hash function binary matrix

       --timing=Timing
               file Print timing information

       --stats=Stats
               file Print stats

       --usage
               Usage

       -h,--help
               This message

       --full-help
               Detailed help

       -V,--version
               Version

   STATS
       Usage: jellyfish stats [options] db:path

       Statistics

       Display some statistics about the k-mers in the hash:

       Unique:  Number of k-mers which occur only once.  Distinct: Number of k-mers, not counting
       multiplicity.  Total: Number of k-mers, including multiplicity.  Max_count: Maximum number
       of occurrence of a k-mer.

       Options (default value in (), *required):

       -L,    --lower-count=uint64
               Don't consider k-mer with count < lower-count

       -U,    --upper-count=uint64
               Don't consider k-mer with count > upper-count

       -v,--verbose
               Verbose (false)

       -o,    --output=string
               Output file

       --usage
               Usage

       -h,--help
               This message

       --full-help
               Detailed help

       -V,--version
               Version

   HISTO
       Usage: jellyfish histo [options] db:path

       Create an histogram of k-mer occurrences

       Create  an  histogram  with  the  number of k-mers having a given count. In bucket 'i' are
       tallied the k-mers which have a count 'c' satisfying 'low+i*inc  <=  c  <  low+(i+1)*inc'.
       Buckets in the output are labeled by the low end point (low+i*inc).

       The  last  bucket  in the output behaves as a catchall: it tallies all k-mers with a count
       greater or equal to the low end point of this bucket.

       Options (default value in (), *required):

       -l,    --low=uint64
               Low count value of histogram (1)

       -h,    --high=uint64
               High count value of histogram (10000)

       -i,    --increment=uint64
               Increment value for buckets (1)

       -t,    --threads=uint32
               Number of threads (1)

       -f,--full
               Full histo. Don't skip count 0. (false)

       -o,    --output=string
               Output file

       -v,--verbose
               Output information (false)

       --usage
               Usage

       --help
               This message

       --full-help
               Detailed help

       -V,--version
               Version

   DUMP
       Usage: jellyfish dump [options] db:path

       Dump k-mer counts

       By default, dump in a fasta format where the header is the count and the sequence  is  the
       sequence of the k-mer. The column format is a 2 column output: k-mer count.

       Options (default value in (), *required):

       -c,--column
               Column format (false)

       -t,--tab
               Tab separator (false)

       -L,    --lower-count=uint64
               Don't output k-mer with count < lower-count

       -U,    --upper-count=uint64
               Don't output k-mer with count > upper-count

       -o,    --output=string
               Output file

       --usage
               Usage

       -h,--help
               This message

       -V,--version
               Version

   MERGE
       Usage: jellyfish merge [options] input:string+

       Merge jellyfish databases

       Options (default value in (), *required):

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

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

       --out-counter-len=uint32
               Length (in bytes) of counting field in output (4)

       --out-buffer-size=uint64
               Size of output buffer per thread (10000000)

       -v,--verbose
               Be verbose (false)

       --usage
               Usage

       -h,--help
               This message

       -V,--version
               Version

   QUERY
       Usage: jellyfish query [options] db:path

       Query from a compacted database

       Query a hash. It reads k-mers from the standard input and write the counts on the standard
       output.

       Options (default value in (), *required):

       -C,--both-strands
               Both strands (false)

       -c,--cary-bit
               Value field as the cary bit information (false)

       -i,    --input=file
               Input file

       -o,    --output=file
               Output file

       --usage
               Usage

       -h,--help
               This message

       -V,--version
               Version

   QHISTO
       Usage: jellyfish qhisto [options] db:string

       Create an histogram of k-mer occurrences

       Options (default value in (), *required):

       -l,    --low=double
               Low count value of histogram (0.0)

       -h,    --high=double
               High count value of histogram (10000.0)

       -i,    --increment=double
               Increment value for buckets (1.0)

       -f,--full
               Full histo. Don't skip count 0. (false)

       --usage
               Usage

       --help
               This message

       -V,--version
               Version

   QDUMP
       Usage: jellyfish qdump [options] db:path

       Dump k-mer from a qmer database

       By default, dump in a fasta format where the header is the count and the sequence  is  the
       sequence of the k-mer. The column format is a 2 column output: k-mer count.

       Options (default value in (), *required):

       -c,--column
               Column format (false)

       -t,--tab
               Tab separator (false)

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

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

       -v,--verbose
               Be verbose (false)

       -o,    --output=string
               Output file

       --usage
               Usage

       -h,--help
               This message

       -V,--version
               Version

   QMERGE
       Usage: jellyfish merge [options] db:string+

       Merge quake databases

       Options (default value in (), *required):

       -s,    --size=uint64
               *Merged hash table size

       -m,    --mer-len=uint32
               *Mer length

       -o,    --output=string
               Output file (merged.jf)

       -p,    --reprobes=uint32
               Maximum number of reprobes (62)

       --usage
               Usage

       -h,--help
               This message

       --full-help
               Detailed help

       -V,--version
               Version

   CITE
       Usage: jellyfish cite [options]

       How to cite Jellyfish's paper

       Citation of paper

       Options (default value in (), *required):

       -b,--bibtex
               Bibtex format (false)

       -o,    --output=string
               Output file

       --usage
               Usage

       -h,--help
               This message

       -V,--version
               Version

VERSION

       Version: 1.1.4 of 2010/10/1

BUGS

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

       *      The  hash  table  does  not grow in memory automatically and jellyfish merge is not
              called automatically on the intermediary files (if any).

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