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).
Uses pbzip2
On Ubuntu you can install most of these software: $ sudo apt-get install pbzip2
Uses some perl libraries so:
$ sudo cpan Data::Dumper threads Getopt::Long Pod::Usage Digest::MD5 BSD::Resource FindBin
For Blue we will need mono:
$ sudo apt-get install mono-runtime mono-mcs
Finally to compile 3rd party software, run make
$ make
$ preprocess_illumina.pl etc
or for pairs: $ preprocess_illumina.pl -paired
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/