libdna VS htslib

While that works for the canonical bases your method won't support CCN which should give Proline. Hence, for my implementation I have opted for a slower but more general approach. As protein coding sequences are usually short performance isn't an issue, really.

In Bioinformatics, if you now the number of mismatching characters between two strings of DNA your can compute their evolutionary distance. As DNA is long, easily a few megabytes, computing such a hamming distance via SIMD really pays of. Here is my implementation if anyone is interested: https://github.com/kloetzl/libdna

There is another nice multi-core gzip based library called BGZF[1]. It is commonly used in bioinformatics. BGZF has the added advantage that it is block compressed with built in indexing method to permit seeking in compressed files.

[1] https://github.com/samtools/htslib

In contrast, processing can start immediately and only transfer what is necessary if tooling can read bytes of data directly from Amazon S3. Tools based on htslib can do this, so you can run something like:

Another idea is add in reading cloud data natively e.g. htslib which samtools relies on can read s3 directly. https://github.com/samtools/htslib

Greetings! I'm a bioinformatics software dev in San Francisco and I'm looking for others interested in working on a high-performance genetic data analysis project. The project is in C, using https://github.com/samtools/htslib.

I'm working on a bioinformatics-related binding called ruby-htslib. htslib makes heavy use of bit fields throughout the library, so supporting bit fields is inevitable.