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Q: What is the max. number of mismatches NextGenMap can handle?
A: NextGenMap doesn’t have a fixed upper limit for mismatches. With default settings NextGenMap can map each read that has at least one stretch of 13bp in common with the reference. However, per default NextGenMap only reports a read as mapped if more than 50% of the bases of the read could be mapped and the alignment has an identity higher than 65%.
Q: I have a read that matches the reference sequence perfectly, why does NextGenMap not map the read?
A: NextGenMap excludes all k-mers that occur more than 1,000 times in the reference genome. If a read only consist of k-mers that occur more than 1,000 times on the genome NextGenMap won’t map it.
Q: Will NextGenMap run on a desktop computer?
A: Yes. In fact NextGenMap is able to adapt to the available hardware. Thus is will work on desktop as well as on server machines. If your desktop computer is equipped with a GPU we recommend you to specify the -g/ --gpu parameter when running NextGenMap. Please see Documentation for more details.
Q: Is it possible to use NextGenMap without a GPU?
A: Running NextGenMap without a GPU is the default mode. Please note that at the moment @-bs-mapping@ is not supported without a GPU. Support for CPU base --bs-mapping will be added in the future.-
Q: Which GPUs are compatible with NextGenMap?
A: NextGenMap requires a CUDA enabled NVidia or an AMD APP enabled ATI GPU. See here for a detailed list.
Q: How can i tell NextGenMap to use my GPU?
A: Use the -g/--gpu parameter. Please see Documentation for more details.
Q: I have a question/comment/problem/suggestion. Who should I contact?
A: Please contact either [email protected] or [email protected]
Q: What are the most sensitive settings for NextGenMap?
A: Parameters: ngm --kmer-skip 0 -s 0.0
With these settings NextGenMap will use all the seed words present in the genome to build the index. In addition, one seed word match is enough to consider a region on the genome a possible mapping region. Therefore, these settings will dramatically increase runtime and only work for small genomes.
Please note that we don’t recommend using these settings.