This is an old (well-cited) paper from 2002, but the algorithm is finding plenty of use lately with SPAdes and Jared Simpson’s nanopolish. I have not checked what algorithm Jason Chin uses in his pbdagcon.
Motivation: Progressive Multiple Sequence Alignment (MSA) methods depend on reducing an MSA to a linear profile for each alignment step. However, this leads to loss of information needed for accurate alignment, and gap scoring artifacts.
Results: We present a graph representation of an MSA that can itself be aligned directly by pairwise dynamic programming, eliminating the need to reduce the MSA to a profile. This enables our algorithm (Partial Order Alignment (POA)) to guarantee that the optimal alignment of each new sequence versus each sequence in the MSA will be considered. Moreover, this algorithm introduces a new edit operator, homologous recombination, important for multidomain sequences. The algorithm has improved speed (linear time complexity) over existing MSA algorithms, enabling construction of massive and complex alignments (e.g. an alignment of 5000 sequences in 4 h on a Pentium II). We demonstrate the utility of this algorithm on a family of multidomain SH2 proteins, and on EST assemblies containing alternative splicing and polymorphism.
Availability: The partial order alignment program POA is available at http://www.bioinformatics.ucla.edu/poa.
Jared posted his code and instructions here.
Brief usage instructions
The pipeline is still a prototype so it is fragile at the moment. It will be revised for general use after we submit the paper.
The reads that are input into the HMM must be output as a .fa file by poretools. This is important as poretools writes the path to the original .fast5 file (containing the signal data) in the fasta header. These paths must be correct or nanopolish cannot find the events for each read. Let’s say you have exported your reads to reads.fa and you want to polish draft.fa. You should run:
make -f consensus.make READS=reads.fa ASSEMBLY=draft.fa
This will map the reads to the assembly with bwa mem -x ont2d and export a file mapping read names to fast5 files.