Novopile is a c++ tool for direct processing of the novoalign output, creating a pileup file designed to match the MAQ pileup output. Novopile can directly process gzipped file, useful given the size of the novoalign output files. In addition to the novoalign output, the user must also provide a query file, indicating the SNPs one wants the output for. The format is simply:
seq1 pos1 ref1
seq2 pos2 ref2
seqn posn refn
The third column is the reference allele from the target reference genome. There can be more columns, and these should be ignored by the software. Otherwise just running ./novoPile should provide all the various options.
In particular, The user can also specify an output file to get all the small indels. Another option is to specify an output file to obtain summary information about the novoalign output (mapping qualities, base composition…).
Novophase is a tool used to phase sequencing data using short reads. Options are similar to novoPile and it looks for paired read that overlap two heterozygous SNPs. This information allows the phasing of these two SNPs.
Download from user site Novopile