Just_Preprocess_My_Reads Code
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| File | Date | Author | Commit |
|---|---|---|---|
| 3rd_party | 2016-04-25 |
Alexie Papanicolaou
|
[594f15] fix2 |
| dbs | 2015-11-07 |
Alexie Papanicolaou
|
[c69a61] update |
| docs | 2015-08-16 |
Alexie Papanicolaou
|
[67fd7c] doco |
| test | 2015-09-03 |
Alexie Papanicolaou
|
[4c3cf3] updaet |
| .project | 2013-11-17 |
Alexie
|
[1808dd] Documentation |
| LICENSE | 2014-04-17 |
Alexie Papanicolaou
|
[722fe8] license apache |
| Makefile | 2016-04-25 |
Alexie Papanicolaou
|
[7320f7] makefile |
| README.md | 2015-09-03 |
Alexie Papanicolaou
|
[f9b3b9] added blue |
| preprocess_illumina.pl | 2016-10-19 |
Alexie Papanicolaou
|
[4faf9f] sed not used if -noconvert |
| preprocess_illumina_automatic.pl | 2015-08-30 |
Alexie Papanicolaou
|
[8ec2ed] update |
| rename_SRA_orig_fastq.pl | 2015-11-07 |
Alexie Papanicolaou
|
[c69a61] update |
| rename_SRA_trimmed_fastq.pl | 2015-11-07 |
Alexie Papanicolaou
|
[c69a61] update |
Read Me
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
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
USAGE
$ preprocess_illumina.pl <infile> <infile2> etc </infile2></infile>
or for pairs:
$ preprocess_illumina.pl -paired <infile1> <infile2></infile2></infile1>
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/
