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dotnetbio
Bioinformatics library for .NET
Is it possible to consider an implementation of the Burrows-Wheeler Aligner (BWA), considering it's one of the most popular open-source sequence mapping packages available and is currently only available via...
I've seen a situation pop up numerous times where the length of the final consensus sequence when calling the following code, changes, if the sequences are ordered from longest to...
I've got come code which parses many intervals from a bam file, with calls to the ParseRange() method. The results are correct, but slower than expected. Reading through the source...
Today I used dotnetbio to parse a bam file. In rare instances (for a total of 3 reads out of 1 million), BamParser.Parse() returned a null object rather than a...
I have noticed that when I try to parse a ClustalW file, it only parses the first set of alignments and ignores all the rest. Is this a common issue...
A low-priority issue, but it would be nice to eventually add the three-letter abbreviations for amino acids to the `aminoAcidValueMap` in `ProteinAlphabet`.
Bio.Algorithms.Translation.Codons contains the standard genetic code. Should there be a second codon map for mitochondrial genes? AGA and AGG are terminating codons in mitochondria, and UGA codes for tryptophan.
There's a check for GFF parsing that requires version 2. The parser works fine for version 3 (default version for Ensembl now), since the attributes are stored as free text....
Are you planning to integrate a VCF parser, or is there another parser I could use for VCF files? I see there's one in development over on this repository: https://github.com/evolvedmicrobe/Bio.VCF....
This is a wonderful library of functions for bioinformatic analysis. I'm excited to try it out! Do you have any plans to implement an alignment algorithm similar to [STAR](https://github.com/alexdobin/STAR), which...