JELLYFISH(1)

NAME

Jellyfish is a 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 occuring 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 occurences

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