rHAT is a seed-and-extension-based noisy long read alignment tool. It is suitable for aligning 3rd generation sequencing reads which are in large read length with relatively high error rate, especially Pacbio’s Single Molecule Read-time (SMRT) sequencing reads.
Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.
Noisy is a software to identify homo-plastic characters in multiple sequence alignments.In a first phase the rows of the input multiple sequence alignment (MSA) in multi fasta format are reordered to conform to a circular ordering. For this purpose noisy includes the corresponding subset of routines from David Bryant and Vincent Moulton’s NeighborNet and Stefan Grünewald’s QNet packages. Subsequently, a reliability score for each column of the reordered MSA is calculated. Essentially, the number of character state alterations in an alignment column is counted and compared to the observed count in random shufflings of the column. The uniform pseudo-random number generator Mersenne Twister is used to generate the random shufflings of alignment columns.
