JELLYFISH(1)

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JELLYFISH(1) 💖

k-mer counter · the jellyfish(1) manual, bestie edition 🪼

✨ NAME ✨

jellyfish — 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. That's it, that's the whole vibe. 🫶

🌸 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

So what's happening here? 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. No cap, we're doing it. 🔥

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. Do not skip this step, bestie, I'm begging. 😭

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. Lowkey just re-run it, it's the move. 💅

🦋 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. Iconic behaviour, honestly. 👑

🎀 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. Main character energy: fit everything, write nothing. ✨

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. So fancy, so convenient. 💖

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. Math girlies, this one's for you. 🧚

💜 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 occurring 2 million times will have a value reported of 2 million (i.e., it is not capped at 2^5). Read that again. Not capped. Periodt.

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. It's giving ✨balance✨.

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 ✨

okay so jellyfish is literally a whole friend group of subcommands, and each one has its own little menu. default values are in (), and a * means required — no skipping those, bestie. 💅

🧮 COUNT 🧮

Usage:

jellyfish count [options] file:path+

Count k-mers or qmers in fasta or fastq files. yes ma'am, the main character of the operation. 👑

Options (default value in (), *required):

  • -m, --mer-len=uint32 — Length of mer (required) 🫶
  • -s, --size=uint64 — Hash size (required) 🫶
  • -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 occurrences.

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 (required) 🫶
  • -m, --mer-len=uint32 — Mer length (required) 🫶
  • -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).

(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

That's the whole vibe, bestie — k-mer counter energy, version 1.1.4 dated 2010/10/1, and yes, it's JELLYFISH(1). Periodt. 💅✨

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