Mercurial > repos > jjohnson > fastqc
comparison fastqc/README @ 0:1d373f219445 default tip
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author | jjohnson |
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date | Tue, 07 Jun 2011 17:22:05 -0400 |
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2 FastQC | |
3 ------ | |
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5 From the FastQC website http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/ | |
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7 Function A quality control tool for high throughput sequence data. | |
8 Language Java | |
9 Requirements A suitable Java Runtime Environment | |
10 The Picard BAM/SAM Libraries (included in download) | |
11 Code Maturity Stable. Mature code, but feedback is appreciated. | |
12 Code Released Yes, under GPL v3 or later. | |
13 Initial Contact Simon Andrews | |
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15 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. | |
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17 The main functions of FastQC are: | |
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19 - Import of data from BAM, SAM or FastQ files (any variant) | |
20 - Providing a quick overview to tell you in which areas there may be problems | |
21 - Summary graphs and tables to quickly assess your data | |
22 - Export of results to an HTML based permanent report | |
23 - Offline operation to allow automated generation of reports without running the interactive application | |
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25 Download and installation information is at: http://www.bioinformatics.bbsrc.ac.uk/projects/download.html#fastqc | |
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28 Galaxy Tool Wrapper | |
29 ------------------- | |
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31 The galaxy tool wrapper for FastQC requires version: FastQC v0.7.2 | |
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33 FastQC should be downloaded and installed on the system on which it will be executed. | |
34 The PATH environment variable should include the directory in which the fastqc script resides. | |
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36 The fastqc.py wrapper invokes the fastqc script provided in FastQC download, | |
37 and converts the FastQC results into a Galaxy html formatted dataset. | |
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