Benjamin Langmead
Benjamin Langmead
This is a new version of the `download_genomes.py` script that puts them in two layers of nested subdirectories (just under the clade level) so as to keep the number of...
Neither the usage message nor the documentation in README.md explain what are the units of the `[size]` parameter for the `--countmin-size` option. Is it bytes?
The `-L` parameter for the `sketch` subcommand does not work as advertised. I get: ``` sketch: invalid option -- 'L' ``` Followed by usage message. If I replace `-L` with...
It would be great if there was a command that could print a cardinality estimate, perhaps from a single cached sketch (i.e. with `--cache` functionality). This was possible before with...
Updates including the switch to Bowtie 2 indexes, the addition of new LevioSAM news and indexes, etc
The Bowtie manual page seems to have some special characters, probably related to the quote characters: http://bowtie-bio.sourceforge.net/manual.shtml#paired-end-alignment. As one example, see: "Paired-end alignments where one mate’s alignment is entirely contained...
It seems that specifying `--debug --sanity` causes `bowtie-build` to hang, or it least it does for every example I just tried, including simple examples. This seems to be the case...
Also robustifies to presence of multiple newlines between raw records.
I made several updates to the index sidebar and added a news item regarding levioSAM
The rule-of-3 lecture ignores move semantics (because I don't actually have time to cover this when I teach in person). But in this day and age, it's probably important to...