{"repo":"tlemane/kmtricks","free":true,"listed":false,"github":"https://github.com/tlemane/kmtricks","clone":"git clone https://github.com/tlemane/kmtricks.git","description":"modular k-mer count matrix and Bloom filter construction for large read collections","language":"C++","stars":89,"topics":["kmer","count","matrix","bloom-filters"],"license":"AGPL-3.0","category":"chat-messaging","readme_excerpt":"kmtricks kmtricks is a modular tool suite for counting kmers, and constructing Bloom filters or kmer matrices, for large collections of sequencing data. Citation Lemane, T., Medvedev, P., Chikhi, R., & Peterlongo, P. (2022). kmtricks: Efficient and flexible construction of Bloom filters for large sequencing data collections. Bioinformatics Advances. Rationale kmtricks is optimized for the analysis of multiple FASTA/FASTQ files (gzipped or not). It features: Fast k-mer matrix construction Fast Bloom filters construction Rescues low-abundance k-mers when they are seen in multiple samples Note: for counting kmers from a single file, kmtricks works but is slightly slower than a traditional k-mer counter (e.g. KMC). It is really optimized for merging count information across multiple samples, which traditional k-mer counters cannot do. Overview Input : a set of read sets in FASTA or FASTQ format, gzipped or not. Final output is either: a matrix of kmer abundances. M i,j is the abundance of kmer i in the read set j a matrix of kmer membership. M i,j is the presence (1) or absence (0) of kmer i in the read set j a vector of Bloom filters. M i,j is the presence (1) or absence (0) of the hash value i (line numbers are hash values) in the read set j. In this case, this matrix is provided vertically (one column is a bloom filter corresponding to one dataset). After transposition, this matrix may also be provided horizontally (one line is a Bloom filter corresponding to one dataset). Thi","default_branch":null,"files":null,"tree":[],"storefront":"/r/tlemane","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/tlemane/kmtricks/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."}