Smash++ is a fast utility designed for the identification and visualization of rearrangements in DNA sequences.
To install Smash++, you'll need CMake version 3.5 or higher, along with a compiler that supports C++14.
# Pull the image
docker pull smortezah/smashpp;
# Run the container
docker run -it smortezah/smashppBegin by installing Miniconda. Once installed, execute the following commands:
conda install -c bioconda -y smashpp# Install Git, CMake and g++
apt update && apt install -y git cmake g++;
# Clone the repository and install it
git clone --depth 1 https://github.com/smortezah/smashpp.git;
cd smashpp;
bash install.sh# Install Homebrew, Git and CMake
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)";
brew install git cmake;
# Clone the repository and install it
git clone --depth 1 https://github.com/smortezah/smashpp.git;
cd smashpp;
bash install.shFirst, set up WSL (Windows Subsystem for Linux). After that, clone the Smash++ repository and proceed with the installation as you would on Ubuntu:
git clone --depth 1 https://github.com/smortezah/smashpp.git;
cd smashpp;
./install.shNote
If you encounter permission issues on any operating system, consider using the sudo command.
./smashpp [OPTIONS] -r <REF_FILE> -t <TAR_FILE>For example:
./smashpp -r ref -t tarFor optimal results, it's advisable to select short names for both reference and target sequences.
To explore the available options for Smash++, execute the following command:
./smashppwhich will yield the following:
SYNOPSIS
./smashpp [OPTIONS] -r <REF_FILE> -t <TAR_FILE>
SAMPLE
./smashpp -r ref -t tar -l 0 -m 1000
./smashpp \
--reference ref \
--target tar \
--format json \
--verbose
OPTIONS
Required:
-r, --reference <FILE> reference file (Seq/FASTA/FASTQ)
-t, --target <FILE> target file (Seq/FASTA/FASTQ)
Optional:
-l, --level <INT>
level of compression: 0 to 6. Default: 3
-m, --min-segment-size <INT>
minimum segment size: 1 to 4294967295. Default: 50
-fmt, --format <STRING>
format of the output (position) file: {pos, json}.
Default: pos
-e, --entropy-N <FLOAT>
entropy of 'N's: 0.0 to 100.0. Default: 2.0
-n, --num-threads <INT>
number of threads: 1 to 255. Default: 4
-f, --filter-size <INT>
filter size: 1 to 4294967295. Default: 100
-ft, --filter-type <INT/STRING>
filter type (windowing function): {0/rectangular,
1/hamming, 2/hann, 3/blackman, 4/triangular, 5/welch,
6/sine, 7/nuttall}. Default: hann
-fs, --filter-scale <STRING>
filter scale: {S/small, M/medium, L/large}
-d, --sampling-step <INT>
sampling step. Default: 1
-th, --threshold <FLOAT>
threshold: 0.0 to 20.0. Default: 1.5
-rb, --reference-begin-guard <INT>
reference begin guard: -32768 to 32767. Default: 0
-re, --reference-end-guard <INT>
reference ending guard: -32768 to 32767. Default: 0
-tb, --target-begin-guard <INT>
target begin guard: -32768 to 32767. Default: 0
-te, --target-end-guard <INT>
target ending guard: -32768 to 32767. Default: 0
-ar, --asymmetric-regions
consider asymmetric regions. Default: not used
-nr, --no-self-complexity
do not compute self complexity. Default: not used
-sb, --save-sequence
save sequence (input: FASTA/FASTQ). Default: not used
-sp, --save-profile
save profile (*.prf). Default: not used
-sf, --save-filtered
save filtered file (*.fil). Default: not used
-ss, --save-segmented
save segmented files (*.s[i]). Default: not used
-sa, --save-profile-filtered-segmented
save profile, filetered and segmented files.
Default: not used
-rm, --reference-model k,[w,d,]ir,a,g/t,ir,a,g:...
-tm, --target-model k,[w,d,]ir,a,g/t,ir,a,g:...
parameters of models
<INT> k: context size
<INT> w: width of sketch in log2 form,
e.g., set 10 for w=2^10=1024
<INT> d: depth of sketch
<INT> ir: inverted repeat: {0, 1, 2}
0: regular (not inverted)
1: inverted, solely
2: both regular and inverted
<FLOAT> a: estimator
<FLOAT> g: forgetting factor: 0.0 to 1.0
<INT> t: threshold (number of substitutions)
-ll, --list-levels
list of compression levels
-h, --help
usage guide
-v, --verbose
more information
-V, --version
show version
To explore the options available for the Smash++ Visualizer, enter the following command:
./smashpp vizor
./smashpp -vizwhich will yield the following:
SYNOPSIS
./smashpp viz|-viz [OPTIONS] -o <SVG_FILE> <POS_FILE>
SAMPLE
./smashpp -viz -o simil.svg ref.tar.pos
./smashpp viz \
--output similarity.svg \
--vertical-view \
ref.tar.json
OPTIONS
Required:
<POS_FILE> position file generated by Smash++ (*.pos/*.json)
Optional:
-o, --output <SVG_FILE>
output image name (*.svg). Default: map.svg
-rn, --reference-name <STRING>
reference name shown on output. If it has spaces, use
double quotes, e.g. "Seq label". Default: the name in
the header of position file
-tn, --target-name <STRING>
target name shown on output
-l, --link <INT>
type of the link between maps: 1 to 6. Default: 1
-c, --color <INT>
color mode: {0, 1}. Default: 0
-p, --opacity <FLOAT>
opacity: 0.0 to 1.0. Default: 0.9
-w, --width <INT>
width of the sequence: 8 to 100. Default: 10
-s, --space <INT>
space between sequences: 5 to 200. Default: 40
-tc, --total-colors <INT>
total number of colors: 1 to 255
-rt, --reference-tick <INT>
reference tick: 1 to 4294967295
-tt, --target-tick <INT>
target tick: 1 to 4294967295
-th, --tick-human-readable <INT>
tick human readable: {0: false, 1: true}. Default: 1
-m, --min-block-size <INT>
minimum block size: 1 to 4294967295. Default: 1
-vv, --vertical-view
vertical view. Default: not used
-nrr, --no-relative-redundancy
do not show relative redundancy (relative complexity).
Default: not used
-nr, --no-redundancy
do not show redundancy. Default: not used
-ni, --no-inverted
do not show inverse maps. Default: not used
-ng, --no-regular
do not show regular maps. Default: not used
-n, --show-N
show 'N' bases. Default: not used
-stat, --statistics
save statistics (*.csv). Default: stat.csv
-h, --help
usage guide
-v, --verbose
more information
-V, --version
show version
Once Smash++ is installed, copy its executable file into the example directory and navigate to that directory:
cp smashpp example/;
cd example/This directory contains two sequences, each 1000 bases long: the reference sequence (ref) and the target sequence (tar). To run Smash++ and the visualizer, use the following commands:
./smashpp -r ref -t tar;
./smashpp viz -o example.svg ref.tar.posUpdate: As of version 22.08, Smash++ now supports the JSON format. To utilize this feature, execute the following command:
./smashpp --reference ref --target tar --format json;
./smashpp viz --output example.svg ref.tar.jsonIf you find Smash++ useful in your research, please acknowledge our work by citing the following:
- M. Hosseini, D. Pratas, B. Morgenstern, A.J. Pinho, "Smash++: an alignment-free and memory-efficient tool to find genomic rearrangements," GigaScience, vol. 9, no. 5, 2020. DOI: 10.1093/gigascience/giaa048
Should you encounter any issues, please don't hesitate to let us know.
Smash++ is protected under the GNU GPL v3 license.
Copyright © 2018-2024 Morteza Hosseini.