What technology (both hardware & software) is out there that allows sensitive (BLAST like) and fast alignment of millions of sequences (c.a. 200bp) against multiple reference genomes?
I know there is:
- Normal software blast: Very sensitive but slow for many millions of sequences against multiple human sized references
- Hardware accelerated blast: Sensitive and fast but requires specialized and expensive hardware
- BWA/SNAP/minimap2: Fast, no specialized hardware, but not sensitive enough for all use cases. Achieves speed (partially) trough exact matching on seeds instead of full alignments. Often misses alignments that are discovered via blast.
The use cases are:
- Determining which (c.a. 200bp) sequences are unique or multi-copy on a certain reference
- Lifting over (c.a. 200bp) sequences from one reference genome sequence to another reference genome sequence ( for non model organisms, where no chain files are available that all the lift over tools seem to use).
I am looking to find something that:
- has the quality / sensitivity of normal blast
- fast enough to align millions of sequences
- cost effective
- reliable and user friendly