Join GitHub today
GitHub is home to over 40 million developers working together to host and review code, manage projects, and build software together.Sign up
Fetching latest commit…
Cannot retrieve the latest commit at this time.
|Type||Name||Latest commit message||Commit time|
|Failed to load latest commit information.|
BEETL: Burrows-Wheeler Extended Tool Library Copyright (c) 2013 Illumina, Inc. This software is covered by the "Illumina Non-Commercial Use Software and Source Code License Agreement" and any user of this software or source file is bound by the terms therein Documentation in: doc/BEETL.md *** Release notes *** Version 0.10.0 (17th June 2014) - New beetl-fastq tool to convert FASTQ files into a set of smaller and searchable files (including quality scores and read ids) - Added RLE53 class (run length encoding: 3 bits for base, 5 bits for run length), but RLE44 is still our default BWT format - Beetl-convert handles BWT44 -> BWT53 conversions - Integrated LCP code with main BCR, making it faster - Beetl-extend can now rebuild the whole reads' bases with --propagate-sequence (instead of stopping at the $ signs) - Replaced compile-time PROPAGATE_SEQUENCE with runtime --propagate-sequence in beetl-compare - Beetl-compare output now correctly goes into the directory specified by --output - Beetl-search/beetl-extend --use-shm stores pre-parsed index files in shared memory for faster tool startup when doing many small searches + Thanks to Shaun Jackman and Rayan Chikhi for compilation patches Version 0.9.0 (9th December 2013) - New K-mer search and propagation tools (see example with beetl-search/beetl-extend in doc/BEETL.md) - MetaBeetl filtering changed a bit, in preparation for further improvements - MetaBeetl database construction scripts and instructions updated - Better distribution packaging, with "make distcheck" Version 0.8.0 (29th October 2013) - New BWT-based tumour-normal filter (see example in doc/BEETL.md) - Beetl-compare modes: 'split' renamed to 'splice' - Beetl-compare modes: new 'tumour-normal' - 16-way parallel backtracker/beetl-compare - MetaBEETL is now able to run without sequence propagation (which is faster) - Upgraded requirement: autoconf 2.65 (improved regression testing) Version 0.7.0 (18th September 2013) - New beetl-correct tool - Updated regression tests - Detection of required libraries and OpenMP in configure script Version 0.6.0 (27th August 2013) - Important: Harmonised file encodings: you may need to rebuild your BWT files or just convert bwt-B00 from BWT_ASCII to BWT_RLE with beetl-convert (bwt-B00 was always ASCII-encoded. It now follows the same encoding as the other piles) - Now requires GCC with C++11 support (gcc 4.6 or above) - New Markdown documentation style - Faster beetl-compare and metaBEETL - Lossless quality compression scripts added, even though they are not using BWT - New features: - BWT creation with reverse-complemented reads (--add-rev-comp) - BWT creation with multiple reads per sequence (--sequence-length) - Support for BCL and BCL.gz in beetl-convert Version 0.5.0 (10th June 2013) - Faster metaBEETL - Pruning of BKPT to reduce the number of MTAXA tests and output lines - New beetl-compare --subset obtion for distributed computing Version 0.4.0 (10th April 2013) - Robustness improvements Version 0.3.0 (7th April 2013) - Metagenomics 'META-BEETL' code added to main tree Version 0.2.0 (19th March 2013) - Longest Common Prefix computation integrated under --generate-lcp in beetl-bwt - New beetl-unbwt command line interface Version 0.1.0 (28th February 2013) - New command line interface - Support for FASTA, FASTQ, raw SEQ and cycle-by-cycle files as input - Distinct intermediate and final formats - Support for Huffman encoding as intermediate or final format - Support for intermediate "incremental run-length-encoded" format - Automatic detection of format - Performance prediction for automatic use of fastest algorithm and options Version 0.0.2 (25th June 2012) Version 0.0.1 (18th November 2011) This contains initial implementations of the BCR and BCRext algorithms as described in our CPM paper. *** Contributors *** Markus J. Bauer, Illumina UK Anthony J. Cox, Illumina UK (project lead) Tobias Jakobi, University of Bielefeld Giovanna Rosone, University of Palermo Ole Schulz-Trieglaff, Illumina UK Lilian Janin, Illumina UK *** Citation *** Markus J. Bauer, Anthony J. Cox and Giovanna Rosone Lightweight BWT Construction for Very Large String Collections. Proceedings of CPM 2011, pp.219-231