{"repo":"Rbfinch/grepq","free":true,"listed":false,"github":"https://github.com/Rbfinch/grepq","clone":"git clone https://github.com/Rbfinch/grepq.git","description":"quickly filter fastq files by matching sequences to a set of regex patterns","language":"Rust","stars":60,"topics":["bioinformatics","fastq","grep","grep-like","grep-search","grepping","gzip","json","regex","sqlite"],"license":"MIT","category":"databases-storage","readme_excerpt":"Quickly filter FASTQ files Table of Contents - Feature set - Features and performance in detail - Usage - Preparing pattern files - Requirements - Installation - Examples and tests - Further testing - Citation - Update changes - Contributing and issue reporting - License Feature set [!NOTE] This README contains documentation for the latest version of grepq . If you are working through this documentation and the examples, please ensure that you are using the latest version. You can check the version by running grepq -V . For installation instructions, see the Installation section. - very fast and scales to large FASTQ files - IUPAC ambiguity code support - support for gzip and zstd compression - JSON support for pattern file input and tune and summarise command output, allowing named regex sets, named regex patterns, and named and unnamed variants - use predicates to filter on the header field (= record ID line) using a regex, minimum sequence length, and minimum average quality score (supports Phred+33 and Phred+64) - does not match false positives - output matched sequences to one of four formats - optionally output matched sequences to a SQLite database file, including GC content, tetranucleotide and canonical tetranucleotide frequencies, and regex pattern matches and their position(s) in each matched FASTQ sequence, allowing for further analysis - tune your pattern file and enumerate named and unnamed variants with the tune command (use the summarise command to process all","default_branch":null,"files":null,"tree":[],"storefront":"/r/Rbfinch","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/Rbfinch/grepq/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."}