Mercurial > repos > jjohnson > fastqc
annotate 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 |
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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. |
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8 Language Java |
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9 Requirements A suitable Java Runtime Environment |
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10 The Picard BAM/SAM Libraries (included in download) |
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11 Code Maturity Stable. Mature code, but feedback is appreciated. |
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12 Code Released Yes, under GPL v3 or later. |
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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) |
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20 - Providing a quick overview to tell you in which areas there may be problems |
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21 - Summary graphs and tables to quickly assess your data |
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22 - Export of results to an HTML based permanent report |
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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 |
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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. |
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34 The PATH environment variable should include the directory in which the fastqc script resides. |
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35 |
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36 The fastqc.py wrapper invokes the fastqc script provided in FastQC download, |
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37 and converts the FastQC results into a Galaxy html formatted dataset. |
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