Do you know a software that can use a sequence as reference to initiate a mapping but then just use overlapping with previous reads to extend the mapping ? Like in a iterative seed-extension process? Starting from a short (maybe 50bp) seed?
What kind of data do you have? This is also a Question, as Tool is for announcing new software.
Paired-end short reads. Sorry for the missclassification.
Isn't that what all of the standard NGS aligners do, seeding and re-seeding? bwa mem, bowtie2, hisat2 etc...
What I need is to go beyond my reference. For example, I have 50bp well-conserved between the reference and then a big insertion. I want to retrieve reads that matched the 50pb probe and then use the overhangs end to extend my sequence. this part is not similar to the ref so it wouldn't be a match. I think aligners jsut map to a ref. The result is not longer than the reference, is it?
you might get some ideas/pointers when looking into the gapfilling tools (part of the assembly process). What you describe is exactly what most of them do
Thank you, I have. Works well if you have two extremeties to fill. In cases where I only have the start of the sequence or the end, they are not useful.
I discovered Geneious mapper can do that, map on a reference then use the consensus to extend the mapping process iteratively. Works well but I'd like to find something I can use on hundred of sequences (command line) instead of manually in GUI.
though I do think some of them might do this as well, I see your point.
What about an assembly tool then? (will likely not be ideal either)
Depending on how much sequences you have to process you might consider one of the very old seed-en-extent software? something like cap3 for instance?
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