Download Latest Version
justpreprocessmyreads_Aug2015c.tar.gz (27.4 MB)
Get an email when there's a new version of Just_Preprocess_My_Reads
| Name | Modified | Size | Downloads / Week |
|---|---|---|---|
| older | 2014-01-16 | ||
| justpreprocessmyreads_Aug2015c.tar.gz | 2015-08-31 | 27.4 MB | |
| README.md | 2015-08-17 | 1.2 kB | |
| Totals: 3 Items | 27.4 MB | 0 |
Alexie's Illumina preprocessing pipeline; no warranty but we use it... complaints to alexie@butterflybase.org
Identifies rRNA, contaminants, trims in a standard fashion etc. Maintains read pairs. Built for fire-and-forget high throughput projects (terabytes of data).
INSTALL
Run make
$ make
Uses pbzip2
On Ubuntu you can install most of these software: $ sudo apt-get install pbzip2
USAGE
$ preprocess_illumina.pl <infile> <infile2> etc
or for pairs: $ preprocess_illumina.pl -paired <infile1> <infile2>
see $ perldoc preprocess_illumina.pl or code within $ vim preprocess_illumina.pl
+++++++++++++++++++++++++ Programs used:
Trimmomatic http://www.usadellab.org/cms/index.php?page=trimmomatic Lohse M, Bolger AM, Nagel A, Fernie AR, Lunn JE, Stitt M, Usadel B. RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic Acids Res. 2012 Jul;40(Web Server issue):W622-7.
pbzip2 Jeff Gilchrist http://compression.ca Debian/Ubuntu: apt-get install pbzip2
fastqc simon.andrews@babraham.ac.uk http://www.bioinformatics.bbsrc.ac.uk
allpathslg http://www.broadinstitute.org/software/allpaths-lg/blog/