{"repo":"smortezah/smashpp","free":true,"listed":false,"github":"https://github.com/smortezah/smashpp","clone":"git clone https://github.com/smortezah/smashpp.git","description":"Find and visualize rearrangements in DNA sequences","language":"C++","stars":55,"topics":["high-throughput-sequencing","alignment-free","genome-compression","dna-sequences","data-visualization","genome-rearrangment"],"license":"GPL-3.0","category":"deployment-docker-iac","readme_excerpt":"Smash++ Smash++ is a fast utility for identifying and visualizing rearrangements in DNA sequences. Installation Smash++ requires CMake 4.0.0 or newer and a compiler with C++20 support. Conda Docker Build From Source By default, install.sh builds in ./build and installs smashpp , smashpp-inv-rep , and exclude N into ./dist/bin . You can customize the build with environment variables: Ubuntu macOS Windows Install Visual Studio 2022 Build Tools with the Desktop C++ workload, plus Python 3. The PowerShell installer supports the same knobs as the shell script, for example: Usage If you used the default source install, run the binaries from ./dist/bin . For best results, keep the reference and target filenames short. Smash++ Options Use smashpp --help to print the full CLI help. Option Value Description Default ------------------------------------------ -------------- ------------------------------------------------------------------------------------------------------------------------ ------------------- -r , --reference Reference file in seq , FASTA , or FASTQ format. Required -t , --target Target file in seq , FASTA , or FASTQ format. Required -l , --level Compression level from 0 to 6 . 3 -m , --min-segment-size Minimum segment size. 50 -fmt , --format Output format: pos or json . pos -e , --entropy-N Entropy assigned to N bases. 2.0 -n , --num-threads Number of worker threads. 4 -mem , --max-memory Maximum estimated memory use. Supports B , K , M , G , and T suffixes; 0 disab","default_branch":null,"files":null,"tree":[],"storefront":"/r/smortezah","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/smortezah/smashpp/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}