COUNTING AND MERGING

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

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

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

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

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

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

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

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

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

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

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

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

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

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