How to predict stop codons in Illumina reads? I have Illumina MiSeq paired-end reads from 150bp amplicons mapped to my reference genome (> 1000X coverage). These reads have indels that may or may not induce frameshifts. If the indel induces a frameshift (i.e. indel is not a multiple of 3bp), I want to know if that leads to a stop codon later in the read. Is there any package/method that would allow me to do this?

Few extra details


I might be wrong but I think this is different than gene prediction as I would want the tool to scan each read in the correct frame; not try different frames to detect ORFs etc.
I expect mosaicism, so I do not want to compute a single assembly/consensus and predict stop codons in it.


Here is how I imagine such a script/tool would work:


Take the position of the first translated codon of the exon I am interested in (from Ensembl for instance?). Eg. gene abc/exon1 starts at chr1:1000.


Then for each read:


Look at which position the read is mapped to my reference. Eg. read 1 is mapped to chr1:1050.
Compute the position of the first full codon in the correct frame in my read. Eg. start codon at chr1:1000 but my read starts at chr1:1050, the first full translated codon in my read should start at chr1:1052 (I think?).
Split all my read into 3-mers starting at that position and build something like a 3-mer/position dictionnary. 
Look for stop codons and report the positions.


Does it exist?
With 150bp reads, you might be able to blastx all the unique sequences you've got against the target proteins.