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KmerCamel🐫

KmerCamel test

Introduction

KmerCamel🐫 is a tool for efficiently representing a set of k-mers a masked superstring.

It is based on the following paper:

Ondřej Sladký, Pavel Veselý, and Karel Břinda: Masked superstrings as a unified framework for textual k-mer set representations. bioRxiv 2023.02.01.526717, 2023. https://doi.org/10.1101/2023.02.01.526717

See supplementary materials of the aforementioned paper for experimental results with KmerCamel🐫.

The computation of masked superstring using KmerCamel🐫 is done in two steps - first a superstring is computed with its default mask and then its mask can be optimized.

The computation of the masked superstring works as follows. KmerCamel🐫 reads an input FASTA file (optionally gziped), retrieves the associated k-mers (with supported $k$ up to 127), and outputs a fasta file with a single record - a masked-cased superstring, which is in the nucleotide alphabet with case of the letters determining the mask symbols. KmerCamel🐫 implements two different algorithms for computing the superstring: global greedy and local greedy. Global greedy produces more compact superstrings and therefore is the default option, but local greedy requires less memory and hence can be more suitable in use cases where memory is the main limitation.

To compute masked superstrings takes about 4-6s / 1M k-mers, which means about 3h to compute masked superstrings for the human genome. The memory consumption on human genome is about 115 GB.

All algorithms can be used to either work in the unidirectional model or in the bidirectional model (i.e. treat $k$-mer and its reverse complement as the same; in this case either of them appears in the result).

Additionally, KmerCamel🐫 can optimize the mask of the superstring via the optimizesubcommand. The implemented mask optimization algorithms are the following:

  • Minimize the number of 1s in the mask.
  • Maximize the number of 1s in the mask.
  • Minimize the number of runs of 1s in the mask.

Prerequisites

  • GCC
  • Zlib
  • GLPK (can be installed via apt-get install libglpk-dev on Ubuntu or brew install glpk on macOS)

Getting started

Installation

Download and compile KmerCamel🐫 by running the following commands:

git clone --recursive https://github.com/OndrejSladky/kmercamel
cd kmercamel && make

Alternatively, you can install KmerCamel from Bioconda:

   conda install kmercamel

Compression for k-mer set storage

./kmercamel -p yourfile.fa -k 31 -c > ms.fa        # Compute MS with the default mask
cat ms.fa | tr acgt 0000 | tr ACGT 1111 > mask.txt # Extract mask
cat ms.fa | tr acgt ACGT > superstring.txt         # Extract superstring
bzip2 --best mask.txt
xz -T1 -9 superstring.txt

For a super efficient compression of the superstring (often <2 bits / bp), you use some of the specialized tools based on statistical compression such as GeCo3 or Jarvis3.

k-mer set indexing

Example with FMSI:

kmercamel -p yourfile.fa -k 31 -c > ms.fa          # Compute MS with the default mask
kmercamel optimize -p ms.fa -k 31 -c -o ms-opt.fa  # Maximize the number of 1s in the mask
fmsi index -p ms-opt.fa                            # Create a k-mer index

Detailed instructions

Computing masked superstrings:

./kmercamel -p ./spneumoniae.fa -k 31 -c                # From a fasta file
./kmercamel -p - -k 31 -c                               # Read from stdin
./kmercamel -p ./spneumoniae.fa.gz -k 31 -c             # From a gzipped fasta file
./kmercamel -p ./spneumoniae.fa -k 127 -c               # Largest supported k
./kmercamel -p ./spneumoniae.fa -k 31 -a local -d 5 -c  # Use local greedy
./kmercamel -p ./spneumoniae.fa -k 31 -c -o out.fa      # Redirect output to a file
./🐫 -p ./spneumoniae.fa -k 31 -c                        # An alternative if your OS supports it

Optimizing masks:

./kmercamel optimize -p ./masked-superstring.fa -k 31 -a runs -c        # Minimize the number of runs of 1s
./kmercamel optimize -p ./masked-superstring.fa -k 31 -a ones -c        # Maximize the number of 1s
./kmercamel optimize -p ./masked-superstring.fa -k 31 -a zeros -c       # Maximize the number of 0s
./kmercamel optimize -p ./masked-superstring.fa -k 31 -a runapprox -c   # Approximately minimize the number of runs of 1s

Compute lower bound on the minimum possible superstring length of a k-mer set:

./kmercamel -l -p ./spneumoniae.fa -k 31

Additionally, KmerCamel🐫 experimentally implements both algorithms in their Aho-Corasick automaton versions. To use them, add AC to the algorithm name. Note that they are slower than the original versions, but they can handle arbitrarily large ks.

Arguments

The program has the following arguments:

  • -p path_to_fasta - the path to fasta file (can be gziped). This is a required argument.
  • -k value_of_k - the size of one k-mer (up to 127). This is a required argument.
  • -a algorithm - the algorithm which should be run. Either global or globalAC for Global Greedy, local or localAC for Local Greedy. The versions with AC use Aho-Corasick automaton. Default global.
  • -o output_path - the path to output file. If not specified, output is printed to stdout.
  • -d value_of_d - d_max used in Local Greedy. Default 5. Increasing d beyond k has no effect.
  • -c - treat k-mer and its reverse complement as equal.
  • -l - compute lower bound on the superstring length instead of the superstring.
  • -m - turn off memory optimizations for global.
  • -h - print help.
  • -v - print version.

For mask optimization, run the subcommand optimize with the following arguments:

  • p path_to_fasta - the path to fasta file (can be gziped). This is a required argument.
  • k k_value - the size of one k-mer. This is a required argument.
  • a algorithm - the algorithm for mask optimization. Either ones for maximizing the number of 1s, runs for minimizing the number of runs of 1s, runsapprox for approximately minimizing the number of runs of 1s, or zeros for maximizing the number of 0s. Default ones.
  • o output_path - the path to output file. If not specified, output is printed to stdout.
  • c - treat k-mer and its reverse complement as equal.
  • h - print help.
  • v - print version.

Converting k-mer set superstring representation to the (r)SPSS representations

We provide a Python script for converting any masked superstring to a (r)SPSS representation. Run ./convert_superstring.py < input.fa. This runs a Python script which inputs a fasta file with masked-cased superstring and outputs the (r)SPSS representation.

How it works

For details about the algorithms and their implementation, see the Code README.

How to test

To ensure correctness of the results, KmerCamel🐫 has two levels of tests - unit tests and file-specific integration tests.

For integration tests install jellyfish (v2) and add it to PATH.

You can verify all the algorithms for 1 < k < 128 on a S. pneumoniae by running make verify. To run it on another dataset, see the verification script.

You can run the C++ unittests by make cpptest.

To run all the test, simply run make test.

Issues

Please use Github issues.

Changelog

See Releases.

Licence

MIT

Contact

Ondrej Sladky <[email protected]>\