Adventure: Choose your own Adventure in Sequence processing.

Over the few years I have been playing in Dr. El-Sayed's lab, I found myself copy-pasting snippets of Perl for common tasks like sequence alignment, setting up PBS jobs, counting reads, whatever. Eventually, having a large number of these repetitive scripts came to seem stupid. Therefore I combined them into a single Perl package and attempted to give them a single interface: cyoa.

Rebuilding the distribution

dzil build

Installation

git clone git@github.com:abelew/CYOA.git && cd CYOA && perl Makefile.PL && make && make install

If you have some free time:

make test

That will test (currently) the ability to:

• load HPGL.pm
• look for perl requirements
• run fastqc on a small dataset
• run trimomatic on the same data
• run bowtie, convert the sam->bam, and count reads of phix
• test parsing of a tritryp text file
• run tophat for phix
• run bwa for phix
• perform a fasta36 search for some leishmania data
• clean up the mess

Final installation:

make install

Usage

I have recently been using it via a small script 'cyoa' in bin/, for example:

cyoa

brings up a readline menu interface asking what you want to do.

cyoa --query lmajor_cds.fasta --library lmajor_cds.fasta --task align --method fastasplit

Splits the set of annotated coding sequences from lmajor into 200 pieces and aligns them against the library of lmajor_cds sequences. Upon completion, it counts the number of hits and therefore provides a rough metric of the set of multi-copy genes.

cyoa --input test-forward.fastq:test-reverse.fastq --task rnaseq --method fastqc

Runs fastqc

cyoa --input test-forward.fastq:test-reverse.fastq --task rnaseq --method tophat --species lmajor

Runs tophat using some generic options with databases specific for L.major.

cyoa --query test.fasta --task alignment --method blastsplit --blast_tool blastp --library nr

Splits test.fasta into a bunch of pieces, aligns them against nr using blastp

cyoa --input test.fastq --task tnseq --method sort --indexfile indexes.txt

Sorts test.fastq using a set of index->samples in indexes.txt

cyoa --input test_forward.fastq:test_reverse.fastq --task pipeline --method priboseq --species lmajor

Performs a ribosome profiling pipeline of steps to fastqc the data, trim it, graph the qualities etc, rRNA search the data, align the non-rRNA against the lmajor genome, convert to bam, and count. It might also try and count the A/P/E sites, I forget if I added that. crap I have to go collect rna.