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Man Pages


Manual Reference Pages  -  JELLYFISH (1)

NAME

Jellyfish is a software to count k-mers in DNA sequences.

CONTENTS

Synopsis
Description
     Counting And Merging
     Orientation
     Choosing The Hash Size
     Choosing The Counting Field Size
Subcommands And Options
     Count
     Stats
     Histo
     Dump
     Merge
     Query
     Qhisto
     Qdump
     Qmerge
     Cite
Version
Bugs
Copyright & License
Authors

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

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k-mer counter JELLYFISH (1) 2010/10/1

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