ViReMa Files

Updates to ViReMa version 0.2


New commandline options:

Chunking:  in the mapping phase of ViReMa (ViReMa.py), the original dataset will be analysed in chunks containing reads of the chosen size.  As reads are mapped independently from one another this does not affect the output.  However, this allows much larger files to be analysed without filling up the temporary memory. Results are appended to the chosen output file after each chunk.

--Chunk 

Enter number of reads to porcess together. Min = 1. Max = number of reads in file.


Choice of bowtie or BWA aligner.  Our results with test data yield identical results when using BWA or bowtie.  The BWA alignment is ungapped.

--Aligner

Enter Alignment Software: 'bwa', 'bowtie'. Default is bowtie.


Rather than having different files.py for each operating system, any Windows user must specify -Win.  This adapts the code accordingly.

-Win

Select this option if running ViReMa from a Windows/Cygwin shell

--X

Number of nucleotides not allowed to have mismatches at 3'  and 5' end of segment. Same as setting --FivePad and --ThreePad seperately.  Default is 5.  See Routh et al.



Other changes:

Substitutions shorter than mismatch tolerance no longer reported as substitutions, but as single mappings if applicable. 

Corrected Mismatch handling Bug in Bowtie parameters.

Add CommandLine Parameters to header in Output file from ViReMa, so may be read directly during second compilation phase.