Description of feature
LAST can align reads to genomes in many-to-one mode, where each base of the reads will match the genome only once. This is neat, since it prevents accumulation of extra alignment coverage at repeat regions. It is not as fast as minimap, but it is handy when the whole LAST pipeline is already setup like here. Also, I like the CRAM output, which play well with the IGV and saves a lot of disk space.
Since 3.0.0, the pipeline accepts FASTQ input and can run this computation. But the one-to-one alignment that it computes is useless in the case of read-to-genome alignment. Also, symmetric scoring matrix should not be enforced since basecalling has strand-specific biases. FASTQ support was only added to open the way to this issue.
Does a read-to-genome mode belong to this pipeline? Maybe as an Easter Egg? Let's see the reception of the PR that will implement it.
Following comments on the review of version 3.0.0, the pipeline argument validation schema should at least be clearer about the file suffixes allowed.
Description of feature
LAST can align reads to genomes in many-to-one mode, where each base of the reads will match the genome only once. This is neat, since it prevents accumulation of extra alignment coverage at repeat regions. It is not as fast as minimap, but it is handy when the whole LAST pipeline is already setup like here. Also, I like the CRAM output, which play well with the IGV and saves a lot of disk space.
Since 3.0.0, the pipeline accepts FASTQ input and can run this computation. But the one-to-one alignment that it computes is useless in the case of read-to-genome alignment. Also, symmetric scoring matrix should not be enforced since basecalling has strand-specific biases. FASTQ support was only added to open the way to this issue.
Does a read-to-genome mode belong to this pipeline? Maybe as an Easter Egg? Let's see the reception of the PR that will implement it.
Following comments on the review of version 3.0.0, the pipeline argument validation schema should at least be clearer about the file suffixes allowed.