Provided as the target sequences, options

Indexing options are fixed in the index file. If even shorter startup time is desired, use this option to save It can index the human genome in a couple

When base-level alignment is not requested, this option is automatically applied.įILE. The index generated with this option will not work with NB: mapping quality is incorrect given aĭont store target sequences in the index. Query.fa multiple times to map it against each batch of target sequences. An HPC sequence is constructed byĬontracting homopolymer runs to a single base. Use homopolymer-compressed (HPC) minimizers. Megabases in length at a error rate ~15%. It works efficiently with query sequences from a few kilobases to ~100 Reference genome optionally with detailed alignment (i.e. Overlaps between long noisy reads, or map long reads or their assemblies to a Minimap2 is a fast sequence mapping and alignment program that can find * Indexing the target sequences (optional):

Minimap2 - mapping and alignment between collections of DNA sequences

Paf reading template