Mark Ebbert

Bug in CMakeLists.txt: cmake does not appropriately throw error if (or opt for dynamic libraries) when static ZLIB missing

3

Hi, I was having trouble compiling ngmlr yesterday. I was getting a linker error because of `ZLIB`: ld: cannot find -lz I was baffled that `cmake` was finding `zlib`, but...

`Samtools + libdeflate` out performs `sambamba` on a single thread

3

Hello, I recently heard about `sambamba` and it's performance gains over `samtools`, and was excited to compare it to `samtools + zlib` and `samtools + libdeflate` (I had also heard...

Hello, Related to #866, we have a specific sample where `bamtofastq` outputs empty reads at the beginning of `fq1` and `fq2` before printing out the rest of the reads. I...

Nextflow not terminating after all tasks completed

11

## Bug report Hello, I submitted a `Nextflow` workflow to our cluster (`SLURM` scheduler), but `Nextflow` did not terminate after all tasks were completed. It eventually timed out because of...

Cigar issue with no M or N between two I's remains in minimap2 v2.26

9

Hello, I posted on issue #392 to try to reopen it since the problem remains in `minimap2` `v2.26`, but the issue remains closed, so I'm opening a new issue. Here's...

Use SigClust to identify significant gene clusters?

3

Hello, We'd like to use SigClust to identify significant gene clusters, also. Is there any fundamental reason we can't use SigClust to do that? i.e., if we simply provide the...

Speed

3

Takes about 30 minutes to run on a 9G fastq file. I've been looking into how we can speed it up. SeqIO.parse populates full SeqRecord objects, but we only need...