We've just put up a new release for download. This release doesn't change Novoalign, it just adds two functions to Novoutil:
- Function iupac merges a VCF file of SNPs into a fasta reference sequence as IUPAC ambiguous codes. Novoalign accepts ambiguous IUPAC codes in the reference and use of this function to incorporate dbSNPs as IUPAC codes increases the accuracy of alignments, reduces allelic bias, and improves accuracy of quality calibration. This utility function is designed to ease the process of creating a suitable reference sequence.
- Function bgzf compresses a file into BAM, tabix, or gzip compatible format using multiple threads or CPUs. If you'd like to save some real time when producing compressed BAM files, or for compressing any file, then you might find this utility useful. Using Picard SortSam with no compression and piped into novoutil bgzf can save 28% of run time.
More information is available on our Wiki page for Novoutil.
We hope you find these useful.
Kind Regards, Colin
Novocraft Technologies Sdn Bhd