Daniel Liu

Sorry for the delay. I've added the conda instructions and the nf-core link to the readme. Thanks for doing this!

Unique reads in this case represents the number of reads with UMIs that are not exactly identical to any other read's UMI. This does not account for errors in the...

If you want to only deduplicate reads if they have the exact same UMI, you should pass in `-k 0` to indicate that zero errors are tolerated.

Yeah, you will need to explicitly specify `sam`/`bam` or `fastq` as the first argument to let UMICollapse know which mode is being used. It seems like UMIs are not being...

@osvaldogc Any updates?

A different simpler evaluation would be to output the pairs of sequences to align from strobealign and plug them into Block Aligner's benchmarks to see if there's a speedup. In...

Try `cargo install --locked --path .`. The README has not been updated yet with this fix. Edit: the README has been updated.

`best` currently only takes BAM files. You can convert your SAM files to BAM files using instructions [here](https://rnnh.github.io/bioinfo-notebook/docs/samtools.html). The reference FASTA file should contain the sequences of the reference (eg.,...

The `--intervals-bed` command can take multiple paths, so it will greedily use all the paths specified afterwards. To work around this, add `--`: ``` best --intervals-bed file.bed -- file.bam file.fna.gz...

Seems like there is an error in parsing the bed file. `best` expects tab separated rows in the bed file. The second and third columns should be integer coordinates. Can...