We like to propose to sequence the genome of your bioinformatician Jason Chin for your ‘The Most Interesting Genome in the World’ contest. Only picture of him available online is shown below.
Jason Chin has been writing amazing open access assembly programs including HGAP, PBdagcon and more recently Falcon. We heard that even your long-read competitor, who pronounced Pacbio dead, uses his programs in their analysis.
Sequencing his genome will help us discover the bioinformatics gene, which we will transfect inside the brain cells of every young biology student to make sure they can assemble long, noisy reads. Or we can even do CRISPR/cas, which seems to be the hottest thing around these days. Going forward, we can even expand this into a larger GWAS project involving those who understand the importance of long reads and those who do not.
As you can see, the possibilities are endless with this small initial investment. Therefore, we earnestly request you to give serious consideration to our proposal.
What is pbdagcon?
pbdagcon is a tool that implements DAGCon (Directed Acyclic Graph Consensus) which is a sequence consensus algorithm based on using directed acyclic graphs to encode multiple sequence alignment.
It uses the alignment information from blasr to align sequence reads to a “backbone” sequence. Based on the underlying alignment directed acyclic graph (DAG), it will be able to use the new information from the reads to find the discrepancies between the reads and the “backbone” sequences. A dynamic programming process is then applied to the DAG to find the optimum sequence of bases as the consensus. The new consensus can be used as a new backbone sequence to iteratively improve the consensus quality.
While the code is developed for processing PacBio(TM) raw sequence data, the algorithm can be used for general consensus purpose. Currently, it only takes FASTA input. For shorter read sequences, one might need to adjust the blasr alignment parameters to get the alignment string properly.
The code and the underlying graphical data structure have been used for some algorithm development prototyping including phasing reads, pre-assembly and a work around to generate consensus from intermediate Celera Assembler outputs.
The initial graphical algorithm was a pure python implementation. Cython was then use to speed it up.
Check out the example/ directory to see how to use it.
Falcon: a set of tools for fast aligning long reads for consensus and assembly
The Falcon tool kit is a set of simple code collection which I use for studying efficient assembly algorithm for haploid and diploid genomes. It has some back-end code implemented in C for speed and some simple front-end written in Python for convenience.