Nils Homer

@markjschreiber Thank-you for the thoughtful response. I have used Parallel Cluster in the past, and what I am trying to avoid is having my clients have to set up and...

Thanks @hmkim87, I have this working in Nextflow and Snakemake, but not through the AGC. The purpose of my request is not to find “A” solution, but to request support...

You may want to check out the `CollectAlternateContigName` tool that parses the NCBI assembly reports: https://github.com/fulcrumgenomics/fgbio/blob/master/src/main/scala/com/fulcrumgenomics/fasta/CollectAlternateContigNames.scala#L108-L137. It stores the mappings in a valid SAM format (SAM header with sequence aliases),...

Would like this too!

@lh3 I'll need advice on what this parameter actually does (for the command line description), as well as if any other parameters are affected. Thanks for any help in advance.

If I add a single mismatch in a read, interestingly I get two contigs. Weird.

I forgot to mention the context. I want to re-assembly a set of reads I know originate from the same haploid copy of the genome, and it's in a tandem...

That is actually what I want, a single contig at then end of the day. Think haploid variant calling across repeat regions with indel and mismatch errors. All reads would...

I am considering using this instead of consensus calling for duplex sequencing. In this case we have stutter due to PCR slippage across STRs.

Also, the introduction in the readme implied it would be suitable for re-assembly if short reads, even in runs of LOH. Would you mind sharing the tuning parameters you tube...