Search Results for "memory"

MuffinEC is an error correction software capable of handling all types of errors (insertion deletions, mismatches and unknown bases). It officially supports four technologies (Illumina, 454, ion Torrent and PacBio - experimental) and it also has a generic setup for others (old and/or new). It is released under LGPL version 3.0. MuffinEC can use multicore systems, thanks to its OpenMP implementation. We are developing the 2nd version of MuffinEC. The beta version is already available...

JFASTA is a lightweight framework for handling FASTA files. It supports reading, writing and parsing of single- or multi-FASTA files. Files may be read/ written at once, or stream-based (memory efficient). It's stable, very intuitive and good integrated with Java 1.5 SDK and later.

PASHA is a parallel short read assembler for large genomes using de Bruijn graphs. Taking advantage of both shared-memory multi-core CPUs and distributed-memory compute clusters, PASHA has demonstrated its potential to perform high-quality de-novo assembly of large genomes in reasonable time with modest computing resources. Our evaluation using three small real paired-end datasets shows that PASHA is able to produce better assemblies with comparable genome coverage and mis-assembly rates compared to three leading assemblers: Velvet, ABySS and SOAPdenovo. ...

...Functions include: duplicate removal demultiplexing primer-removal quality-assurance (QA) graphing quality control (QC) consensus-generation minority-variant determination minority-variant graphing The main current version is 6.X, which is written in Python3. 7.X is my rewrite in Java, but is still work in progress. Both are written to be as lightweight as possible so they can run with minimal memory-requirements on a desktop or laptop as well as on a compute cluster. If you have any problems with QUASR, please do contact me at the email address provided in the README.

GRANULE is a flashcards program based on Leitner cardfile methodology for learning new words. It features long-term memory training capabilities with scheduling, integrated pictures, sound, and full-screen mode.

CLAM is a model of a large-scale cortical network, which incorporates the interaction between object-based and spatial attention and working memory.

CAlib3D is a platform independent library for 3D cellular automata (CA) simulations. It is written in C++. Its advantage is in his speed and memory management.