jellyfish - Online in the Cloud

PROGRAM:

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

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