solexaqa.sourceforge.netSolexaQA - Sequence Quality Statistics and Visualization Tool

: Download Example Graphics FAQsHome ++ Legacy Versions Example Graphics FAQ Download Introduction calculates sequence quality statistics and creates visual representations of data quality for second-generation sequencing data. Originally developed for the Illumina system (historically known as Solexa”), now also supports Ion Torrent and 454 data. Running directly on FASTQ files (now with support for compressed files too), the software has three component algorithms: Analysis — the primary quality analysis and visualization tool. Designed to run on unmodified FASTQ files obtained directly from Illumina, Ion Torrent or 454 sequencers. DynamicTrim — a read trimmer that individually crops each read to its longest contiguous segment for which quality scores are greater than a user-supplied quality cutoff (or alternately, the read segment returned by the BWA trimming algorithm). LengthSort — a program to separate high quality reads from low quality reads. LengthSort assigns trimmed reads to paired-end, singleton and discard files based on a user-defined length cutoff. DynamicTrim and LengthSort are typically used in combination to remove poor quality bases and/or reads from high throughput sequence data. Both programs should work on any FASTQ file (modified or unmodified, compressed or not). The program automatically detects input FASTQ file formats ( i.e. , the Sanger, Illumina and Solexa formats described by Cock et al. 2010 ). It is designed to run on single-end or paired-end data, including reads from the latest versions of the HiSeq and MiSeq machines. High quality graphics are produced by interfacing automatically with R . The software is freely released under the GNU General Public License version 3 . Citation If you use this software, please cite: Cox, M.P., D.A. Peterson, and P.J. Biggs. 2010. : At-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics 11 :485. PDF , Web Link Mailing List We encourage users to join the (low traffic) Google Groups mailing list . Members can discuss the program by sending emails tosolexaqa-users@googlegroups.com . Help will be provided by the software developers, as well as by the user community. Authors was developed by Murray Cox, Patrick Biggs and Daniel Peterson. Release 2.0 was substantially reworked by Mauro Truglio. Release 3.0 was redeveloped in C++ by Mauro Truglio. Please direct questions to Mauro Trugliomauro.truglio@gmail.com , Murray Coxmurray.p.cox@gmail.comor Patrick Biggsp.biggs@massey.ac.nz . Acknowledgments ++ uses Heng Li’s kseq.h library to parse FASTQ files. ++ DownloadRelease 3 is a complete redevelopment of the Perl-based 2 package in the programming language C++. ++ has undergone additional optimization, and the three separate components of the 2 suite (.pl, DynamicTrim.pl and LengthSort.pl) are now presented as options of a single, standalone program, which has been released for a variety of platforms. ++ is no longer dependant on Perl, is cross-platform, and some functions are compatible with sequencing technologies other than Illumina, such as Ion Torrent and 454. All graphics are generated automatically using the award-winning graphical and statistical software R . Changelog v.3.1.7.3: Version 3.1.7.3: Minor update to improve presentation of results. Changelog v.3.1.7.2: Version 3.1.7.2: Minor bugfixes. Changelog v.3.1.7.1: Version 3.1.7.1: Bugfix for high-output NextSeq runs; minor bugfixes. Changelog v.3.1.7: Version 3.1.7: Added support for NextSeq reads. Changelog v.3.1.6: Version 3.1.6: Minor bugfixes. Changelog v.3.1.5: Version 3.1.5: Added subplot to histogram graph that shows the untrimmed length distribution; bugfixes. Changelog v.3.1.4: Bugfix in the analysis heatmap for variable length reads. In case a tile is entirely composed of reads shorter than all the other tiles, the squares for missing cycles are now painted gray. Other minor bugfixes. Changelog v.3.1.3: Bugfix in the analysis histogram for variable length reads; fix for a malloc error on some systems when the -d option with a trailing forward slash is specified in dynamictrim; the summary graph for lengthsort shows the sample(s) name(s) as the graph title. Changelog v.3.1.2: Bugfix in the analysis matrix graph: it now contemplates ".fastq" files in which entire tiles are skipped, and names the tiles that are left correctly on the heat map. Changelog v.3.1.1: Bugfix in LengthSort (single-end mode) Changelog v.3.1: Corrected a file naming bug when operating on .gz files (Linux and Mac only); improved command line output; Analysis : added warning message for SRA-generated fastq files not containing the tile number in the header; DynamicTrim : added the [-a|anchor] option, which allows trimming from the 3’ end only; LengthSort : New naming system for paired end reads: - Read 1 are named "[read1 name].paired" - Read 2 are named "[read2 name].paired" - Single reads are named "[read1 name].single" - Discarded reads are named "[read1 name].discard"; Changelog v.3.0: Analysis (previously available as .pl): general performance improvements; the software can now process FASTQ files with variable read lengths, is compatible with Ion Torrent files (–t option), and .gz compressed files (Linux and OS X releases only). Minor cosmetic changes to graphs and command-line output have also been made. DynamicTrim : general performance improvements (up to 100% faster); bug fix for truncated graphs on variable length reads; compatible with .gz compressed files (Linux and OS X releases only); new progress bar in command-line output. LengthSort : paired-end mode includes a new option (–c) to remove non-matching reads from the two FASTQ files prior to processing; compatible with .gz compressed files (Linux and OS X releases only); new histogram output; new progress bar in command-line output. Warnings: On first use, Linux and OS X users may need to make the ++ file executable ("Permission denied" error). If so, use the command chmod +x ++ The use of compressed (.gz) FASTQ files slows down runtime, especially for large files. Due to library incompatibilities, the Windows version of ++ does not support compressed files. Requirements ++ works across a range of platforms, but is primarily designed for high performance UNIX machines. The program has been released as precompiled binaries for Linux, OS X and Windows, and can be compiled from the source code for other platforms. ++ requires a working (base) installation of R in your PATH in order to produce graphs. Most UNIX systems will already have this program installed. In Windows , R can be downloaded here and placed in the system’s PATH by following this guide . No additional packages or modules are required. Advanced users : to compile from source, ++ requires the g++ compiler, together with the Boost and zlib libraries. Compilation instructions are included in the source code archive. Usage Information Linux and OS X Type the following commands in a console window: ./++ [command] [options] FASTQ_input_file(s) Windows Open a console window (Start → type ’cmd’ → Enter) and type: ++.exe [command] [options] FASTQ_input_file(s) Commands and options: analysis ++ analysis FASTQ input file(s) [-p|probcutoff 0.05] [-h|phredcutoff] [-v|variance] [-m|minmax] [-s|sample 10000] [-b|bwa] [-d|directory path] [sanger illumina solexa] [-t|torrent] OPTIONS: -p or probcutoff FLOAT probability value (between 0 and 1) at which base-calling error is considered too high (default: P = 0.05, or Q ≈ 13) or -h or phredcutoff INT Phred quality score (between 0 and 41) at which base-calling error is considered too high -v or variance calculate variance statistics (note: this approximately doubles the run time) -m or minmax calculate minimum and maximum probabilities for each read position for each tile (note: this increases the run time by ~25%) -s or sample INT integer number of sequences to be sampled per tile for statistics estimates (default: s = 10,000) -b or bwa use BWA...