A new discoSnp++ release is available. http://colibread.inria.fr/software/discosnp/
Existing features in a few words
- Detect SNPs and indels from raw read set(s), without the need of a reference genome.
- Provides genotyping and ranking
- Generates a fasta file of variant predictions containing a micro-assembly of the variant left and rigth neighbors
- Generates a VCF of predicted variants
- Without a reference: no informative prediction locus
- Providing a reference sequence: map predictions. The VCF contains mapping information (locus, multiple matches, …)
- Fast, low memory footprint, easy to use.
New features
- New input format (using file of files)
- Easier to deal with paired datasets
- Easier to simulate file concatenation
- The reference can also be used for calling predictions (not only for mapping them)
- The coverage thresholds can be
- set separately for each read set
- and/or automatically detected for each set
Any comment / remark positive or not is still warmly welcome on the biostar forum