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 documentation is available for you to try before you buy (well download..).

Example Reports

Good Illumina Data

Bad Illumina Data

Adapter dimer contaminated run

Small RNA with read-through adapter

Reduced Representation BS-Seq

PacBio

Changelog

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

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

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

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

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

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