RabbitKSSD is a high-speed genome distance estimation tool with a series of function mudules for genome alalysis, includeing:

• sketch, generate sketch files.
• dist, compute pairwise distances between reference and query genomes.
• set operation, operations on sketches, including subtraction and union.

Installation

RabbitKSSD version 1.0.0 can only support 64-bit Linux Systems.

Dependancy

• cmake v.3.0 or later
• c++14
• zlib
• RabbitFX

Install

• Pay attention to the --recursive option for submodule RabbitFX.
• The install.sh is used for compiling and installing RabbitKSSD.
• The init_shuffle.sh is used for generating the shuffle files and save in the shuf_file/ directory.

git clone --recursive https://github.com/RabbitBio/RabbitKSSD.git
cd RabbitKSSD 
# Compile and install RabbitKSSD
./install.sh
# Init generating the shuffle files
./init_shuffle.sh

Compile from the source code

git clone --recursive https://github.com/RabbitBio/RabbitKSSD.git
cd RabbitKSSD

# Compile rabbitFX library
cd RabbitFX &&
mkdir -p build && cd build &&
cmake -DCMAKE_INSTALL_PREFIX=. .. &&
make -j8 && make install && 
cd ../../ &&

# Compile RabbitKSSD
mkdir -p build
cd build
cmake ..
make -j8 && make install
cd ..

# Init generating the shuffle files
./init_shuffle.sh

Usage

RabbitKSSD has several sub-commands, including shuffle, sketch, alldist, dist, union, sub, convert, merge, and info.
All sub-commands support the -h or --help option for help information.
The sub-command convert is used for converting the sketch format between the Kssd and RabbitKSSD formats.
The sub-command merge is used for merging multiple sketch files into one sketch file.
The sub-command info is used for formatting the sketch files in a human-readable format.
Other sub-commands are introduced in detail in the following sub-sections.

# For help informations:
./rabbit_kssd -h
# It will print:
rabbit_kssd: accelerating Kssd-based genome distance estimation on modern multi-core architectures
Usage: ./rabbit_kssd [OPTIONS] SUBCOMMAND

Options:
  -h,--help                   Print this help message and exit

Subcommands:
  shuffle                     generate the shuffle file for sketching usage
  sketch                      compute sketches for the input genome list
  alldist                     compute all-vs-all distances for one input dataset
  dist                        compute the all-vs-all distances between reference genomes and query datasets
  union                       compute the set union from multiple sketches
  sub                         subtract the reference sketch from the query sketches
  convert                     convert the sketches between Kssd format and RabbitKSSD format
  merge                       merge multiple sketch files into one single sketch file
  info                        get the information of the sketch file

shuffle

The sub-command shuffle is used for generating the shuffle files to create sketches.

-h: For help information.
-k: Half-length of k-mer, -k x means using k-mer of length 2x.
-s: Half-length -f k-mer substring, -s x means the whole space is the collection of all 2x-mer.
-l: Dimension reduction level. -l x means the expected rate of dimensionality reduction is $16^x$.
Users can use init_shuffle.sh to generate the shuffle files automatically.

Recommend:

• -k 8 for bacteria; -k 10 for mammals or metagenomics; -k 9 for other genome size in-between.
• -s 6 is the default setting, usually no need to change this setting; s < k.
• -l 3 for bacteria; -l 4 or -l 5 for mammals; l < s.

# For help information
./rabbit_kssd shuffle -h
# Example:
./rabbit_kssd shuffle -k 10 -s 6 -l 3 -o shuf_file/L3K10.shuf

sketch

The sub-command sketch is used for generating sketches from the input genome list.

-h: For help information.
-L L3K10.shuf: Load the shuffle file L3K10.shuf (k-mer length is 20, dimension reduction level is 3, which means the expected sketch size is $1/16^3$ of the genome size)
-i bacteria.list: Input genome list file bacteria.list, one genome path per line.
-o bacteria.sketch: Output sketch file bacteria.sketch. The hash dictionary file bacteria.sketch.dict and hash offset file bacteria.sketch.index are also generated for distance computation (alldist and dist sub-commands).
-t threads: Set the thread number, default all CPUs of the platform.

# For help information
./rabbit_kssd sketch -h
# Example: 
./rabbit_kssd sketch -L shuf_file/L3K10.shuf -i bacteria.list -o bacteria.sketch

alldist

The sub-command alldist is used for computing the all-vs-all distances for a single genome dataset.

-h: For help information.
-i bacteria.list: Input genome list file bacteria.list, one genome path per line.
-i bacteria.sketch: Input sketch file bacteria.sketch, which is generated by sketch sub-command.
-L L3K10.shuf: Load the shffle file L3K10.shuf for generating sketches.
-D 0.05: Set the maximum output distance threshold, distances over 0.05 are omitted.
-o bacteria.alldist: Set the output distance file bacteria.alldist. When the file is over 4GB, the results are stored to sub-files in bacteria.alldist.dir/ directory, and an appending index file bacteria.alldist.index is generated for retrieving the result.
-t threads: Set the thread number, default all CPUs of the platform.

# For help information:
./rabbit_kssd alldist -h

# Example: computing the all-vs-all distances of bacteria, input as a genome list
./rabbit_kssd alldist -i bacteria.list -L shuf_file/L3K10.shuf -D 0.05 -o bacteria.alldist

is equal to:

# Generating the sketch file:
./rabbit_kssd sketch -L shuf_file/L3K10.shuf -i bacteria.list -o bacteria.sketch
# Computing the all-vs-all distances:
./rabbit_kssd alldist -i bacteria.sketch -D 0.05 -o bacteria.alldist

dist

The sub-command dist is used for computing the all-vs-all distances between the reference and query genome datasets.

-h: For help information.
-r ref.list: Input reference genome list file ref.list, one genome per line.
-r ref.sketch: Input reference sketch file ref.sketch, which is generated by sketch sub-command.
-q query.list: Input query genome list file query.list, one genome per line.
-q query.sketch: Input query sketch file query.sketch, which is generated by sketch sub-command.
-L L3K10.shuf: Load the shuffle file L3K10.shuf for generating sketches.
-D 0.05: Set the maximum output distance threshold, distances over 0.05 are omitted.
-o ref_query.dist: Set the output distance file ref_query.dist. When the file is over 4GB, the results are stored to sub-files in ref_query.dist.dir/ directory, and an appending index file ref_query.dist.index is generated for retrieving the result.
-N 3: Set the maximum number of nearest neighbor reference output for each query genome.
-t threads: Set the thread number, default all CPUs of the platform.

# For help information:
./rabbit_kssd dist -h

Compute the all-vs-all distances between reference and query genome datasets.

# Example: computing the all-vs-all distances between reference and query genome datasets, input as genome list
./rabbit_kssd dist -r ref.list -q query.list -L shuf_file/L3K10.shuf -D 0.05 -o ref_query.dist

is equal to:

# Generating the sketch file:
./rabbit_kssd sketch -L shuf_file/L3K10.shuf -i ref.list -o ref.sketch
./rabbit_kssd sketch -L shuf_file/L3K10.shuf -i query.list -o query.sketch
# Computing the all-vs-all distances:
./rabbit_kssd dist -r ref.sketch -q query.sketch -D 0.05 -o ref_query.dist

Find the nearest neighbor reference for query dataset.

# Example: computing the nearest 3 reference genomes for each query genome
# Input as genome list:
./rabbit_kssd dist -r ref.list -q query.list -L shuf_file/L3K10.shuf -N 3 -o ref_query_nearest_3.dist

# Input as sketch file:
./rabbit_kssd dist -r ref.sktch -q query.sketch -N 3 -o ref_query_nearest_3.dist

union

The sub-command union is used for computing the set union from multiple sketches.

-h: For help information.
-i ref.sketch: Input sketch file ref.sketch, which includes repeated hash values from multiple sketches.
-o ref_union.sketch: Output sketch file ref_union.sketch, which includes a union of hash value set.

# For help information:
./rabbit_kssd union -h
# Example: computing the union of sketch set for ref.sketch
./rabbit_kssd union -i ref.sketch -o ref_union.sketch

sub

The sub-command sub is used for subtracting the reference sketch hash set from each query sketch.

-h: For help information.
--rs human.sketch: Set the reference sketch file human.sketch to be subtracted from the query sketches.
--qs 1000Genomes.sketch: Set the query sketch file 1000Genomes.sketch.
-o: Output sketch file 1000Genomes_sub.sketch, which consists of query sketches after subtraction.
-t threads: Set the thread number, default all CPUs of the platform.

# For help information:
./rabbit_kssd sub -h
# Example:
./rabbit_kssd sub --rs human.sketch --qs 1000Genomes.sketch -o 1000Genomes_sub.sketch

Bug Report

All bug reports, comments and suggestions are welcome.

Cite

Xiaoming Xu, Zekun Yin, Lifeng Yan, Huiguang Yi, Hua Wang, Bertil Schmidt, Weiguo Liu, RabbitKSSD: accelerating genome distance estimation on modern multi-core architectures, Bioinformatics, 2023;, btad695, https://doi.org/10.1093/bioinformatics/btad695