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 $2^5 > 20$.

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