🕷️ Crawler Inspector

 [About](https://www.bioinformatics.babraham.ac.uk/index.html) \| [People](https://www.bioinformatics.babraham.ac.uk/people.html) \| [Services](https://www.bioinformatics.babraham.ac.uk/services.html) \| [Projects](https://www.bioinformatics.babraham.ac.uk/projects/index.html) \| [Training](https://www.bioinformatics.babraham.ac.uk/training.html) \| [Publications](https://www.bioinformatics.babraham.ac.uk/publications.html) ## FastQC | | | |---|---| | Function | A quality control tool for high throughput sequence data. | | Language | Java | | Requirements | A [suitable Java Runtime Environment](https://adoptopenjdk.net/) The [Picard](http://picard.sourceforge.net/) BAM/SAM Libraries (included in download) | | Code Maturity | Stable. Mature code, but feedback is appreciated. | | Code Released | Yes, under [GPL v3 or later](http://www.gnu.org/copyleft/gpl.html). | | Initial Contact | [Simon Andrews](https://www.bioinformatics.babraham.ac.uk/people.html#simon) | | [Download Now](https://www.bioinformatics.babraham.ac.uk/projects/download.html#fastqc) | |  [View our tutorial video](http://www.youtube.com/watch?v=bz93ReOv87Y) FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis. The main functions of FastQC are - Import of data from BAM, SAM or FastQ files (any variant) - Providing a quick overview to tell you in which areas there may be problems - Summary graphs and tables to quickly assess your data - Export of results to an HTML based permanent report - Offline operation to allow automated generation of reports without running the interactive application ## Documentation A [copy of the FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/) documentation is available for you to try before you buy (well download..). ## Example Reports - [Good Illumina Data](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/good_sequence_short_fastqc.html) - [Bad Illumina Data](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/bad_sequence_fastqc.html) - [Adapter dimer contaminated run](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/RNA-Seq_fastqc.html) - [Small RNA with read-through adapter](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/small_rna_fastqc.html) - [Reduced Representation BS-Seq](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/RRBS_fastqc.html) - [PacBio](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/pacbio_srr075104_fastqc.html) - [454](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/454_SRR073599_fastqc.html) ## Changelog - 01-03-23: Version 0.12.0 released - - Fix a bug in file type detection on OSX - 01-03-23: Version 0.12.0 released - - Add total base count to basic stats - Add dup\_length option to set the level of truncation for duplicate finding - Make default truncation length always 50bp - Removed the deduplicated duplication line from the duplicate plot - Improve memory handling and add a --memory option to the command line - Move BAM parsing to htsjdk - Make colours colourblind friendly - Generate SVG versions of graphs, and add a --svg option to use these in the report - Add line numbers to parsing errors - Change the default adapter sequences to search - 08-01-19: Version 0.11.9 released - - Fixed a bug when analysing empty files - Added support for multi-read fast5 files - Fixed a corner case bug in adapter detection - Bundled a JRE with the OSX build so you don't have to install it - Fixed a hang if the program runs out of memory - 04-10-18: Version 0.11.8 released - - Fixed a performance bug in highly duplicated sequences - Changed the behaviour of the sequence length module when run with --nogroup - Other minor bug fixes - 10-01-18: Version 0.11.7 released - - Fixed a crash if the first sequence in a file was shorter than 12bp - 21-12-17: Version 0.11.6 released - - Disabled the Kmer plot by default - Fixed a bug when long custom adapters were being used - Changed the tile number cutoff to accommodate the novaseq - Fixed various format changes in nanopore data from ONT - Added new Clontech sequences to the contaminant list - Added a --min-length option to remove short sequences - Added an option to specify the output name of data streamed into the program - 08-03-16: Version 0.11.5 released - - Fixed the smallRNA adapter sequence so that abundance isn't under-represented in the adapter content plot - Fixed a bug in the warn / error code for the per-base sequence content plot - Fixed a typo in the documentation for the duplication plot - 09-10-15: Version 0.11.4 released - - Changed the OSX launcher to not rely on the internal JVM framework, but use any command line java which is found - Fixed a typo in one of the adapter sequences - Fixed a bug which meant that some file extensions weren't removed from report names in non-interactive mode - Made the per-tile module not collect any stats if it's disabled in limits.txt - Fixed a bug in the calculation of duplication for highly duplicated, ordered files with very small numbers of sequences - Fixed an incorrect error flag in the per-base quality module where there were less than 100 observations in a read group - 25-3-15: Version 0.11.3 released - - Fixed a bug when disabling the per-tile plot from limits.txt - Fixed a bug which caused the program to continue when processing of multiple files was actually complete - Fixed a bug which meant format selection in the interactive application didn't work - Added checks for mis-itentifying tile numbers in confusing sample ids - Added the SOLID smallRNA adapter to the standard search set - Fixed a bug when extracting casava names from uncompressed fastq files - Added support for processing files of Oxford Nanopore reads - 6-6-14: Version 0.11.2 released - - Fixed incorrect warn/fail defaults for per-seq quality plot - Fixed memory leaks in Kmer and per-seq quality modules - Added an option to use a custom limits file - Fixed a bug in the naming of the folder inside the zip output file - Fixed a bug in the --extract option - 2-6-14: Version 0.11.1 released - - Added configurable warn/fail thresholds for all modules - Allow modules to be selectively turned off - Added a per-tile quality plot for Illumina libraries - Added an adapter content plot - Improved the duplication plot - Improved the Kmer module - Used embedded graphics in the HTML output so you can distribute a single file - Added the ability to read data from stdin - Changed how base grouping works to better accommodate long reads - Dropped support for Solexa64 format (NB **not** Phred 64 which is still supported) - 3-5-12: Version 0.10.1 released - - Added a workround to allow the analysis of concatenated gzipped files - Fixed a bug when FastQC was installed in a path containing characters needing to be escaped in a URL - Added an option to specify the location of the java interpreter on the command line - 9-9-11: Version 0.10.0 released - - Added a Casava mode to sanely process the multiple fastq files produced by the latest illumina pipeline - Fixed a bug in Kmer analysis which missed of the last possible Kmer in each sequence - Fixed a classpath bug if using the wrapper script under windows - 31-8-11: Version 0.9.6 released - - Fixed a crash in libraries where every sequence ended in poly-N - Fixed the launch wrapper to set the classpath correctly on OSX - 16-8-11: Version 0.9.5 released - - Fixed a bug in text output for the per-base sequence content module - Made progress reporting absolute, and not approximate - Added a print CSS style so reports are printable again - 13-7-11: Version 0.9.4 released - - Improved the error reporting for failed files in the offline application - 16-6-11: Version 0.9.3 released - - Added support for bzip2 compressed fastq files - Added new CSS theme for HTML reports, contributed by Phil Ewels - 16-5-11: Version 0.9.2 released - - Fixed a bug where grouped base numbers weren't reported in the per-base quality text report - Fixed a crash in the Kmer analysis when analysing small files - 30-3-11: Version 0.9.1 released - - Added --quiet and --nogroup options to command line - Added encoding type to the basic stats - Added detection of Illumina \<1.3 1.3 1.5 and 1.9 encodings - 10-2-11: Version 0.9.0 released - - Added support for very long reads (esp 454 and PacBio) - Duplication detection now uses only the first 50bp of each read - 21-1-11: Version 0.8.0 released - - Made all graphs easier to interpret - Added an option to analyse only mapped sequences from a BAM/SAM file - Added an option to analyse two or more files in parallel - 24-11-10: Version 0.7.2 released - - Fixed bug when analysing libraries with no unique sequences - Added an option to specify a custom contaminant list on the command line - 24-11-10: Version 0.7.1 released - - Improved the command line interface with proper options and error handling - Added an option to force the file format where guessing from the filename doesn't work - 27-10-10: Version 0.7.0 released - - Added a Kmer enrichment analysis to find non-aligned enriched sequences - Cleaned up axis labels on all graphs - 27-10-10: Version 0.6.1 released - - Fixed a bug which caused some sequences and qualities from BAM/SAM files to be reversed - 18-10-10: Version 0.6.0 released - - Sequences can now be read from SAM/BAM format files - Added smoother lines to the graphs - 29-09-10: Version 0.5.1 released - - Fixed a formatting bug in the text output - Fixed the %GC plot to work well with reads over 100bp - Improved the fitting of the modelled curve to the %GC plot - Added more illumina oligos to the contaminants file - 16-09-10: Version 0.5.0 released - - Improved the fitting of the normal distribution to %GC plot - Calculated the total duplicated sequence % in the duplicate sequence module - Added pass/fail/warn icons next to each section of the HTML report - Put Icons and Images into subfolders in the HTML report - 30-07-10: Version 0.4.3 released - - Fixed the reporting of sequence counts in the Basic Stats module - Added a warning before overwriting reports in the interactive application - 26-07-10: Version 0.4.2 released - - Fixed y-axis scale on per-base quality plot - Added fail / warn checks to modules which lacked them and improved existing checks - Added a modelled distribtion to the per-sequence GC plot - Scale the width of report graphs for long sequence reads - 24-06-10: Version 0.4.1 released - - Changed the duplicate module to reduce memory usage for long sequences - Changed the way duplicate levels are counted to be more realistic - 18-06-10: Version 0.4 released - - Added a sequence duplication level module - Added a lauch wrapper for easier use from the commandline - Added full machine parsable output for integration into pipelines - 28-05-10: Version 0.3.1 released - - Fixed a bug where invalid template files caused a crash - Non-interactive use now correctly reports progress for all files, not just the first one - Added some missing documentation - 13-05-10: Version 0.3 released - - Added support for gzip compressed fastq files - Added identification of overrepresented sequences - Improved colorspace support - Added an option to save non-interactive reports to a specific directory - 06-05-10: Version 0.2 released - - Added support for colorspace fastq files - Added templating support to allow customisation of HTML reports - Unzipped non-interactive reports by default, and added an option to turn this off - Added easily computer readable summary file to reports - 28-04-10: Version 0.1.1 released - - Fixed a bug which prevented non-interactive use on a headless system - 26-04-10: Version 0.1 released - - Initial set of 9 modules - Interactive and offline operation functional Having problems with the site? Please [let us know](mailto:simon.andrews@babraham.ac.uk)