Sergey Koren
Sergey Koren
Release 2.1 doesn't work with -trim-assemble and HiFi data on the grid, trimming is skipped prematurely. Using -untrimmed works as expected. Here are the commands: ``` canu -untrimmed -p asm...
There was a user who hit a verkko error with mashmap installed through conda (see: https://github.com/marbl/verkko/issues/162). Couldn't confirm mashmap version since it won't run to report version but I would...
I have a human sample from HPRC (HG01099) where it seems there is incorrect alignment between haplotypes. Here is the region post-resolution: ...
I ran MBG v1.0.14 with the same input corrected HiFi reads, the first run used `--unitig-abundance 2` while the second one used `--unitig-abundance 4`. The run with the higher abundance...
In the new_mbg/bonobo folder, there are 36 t2t scaffolds in the original MBG version vs 24 w/new. The files t2t_scaffolds_by_chr list the t2t scaffolds and their chromosome IDs. These both...
Allow generic tools to request trimmed or untrimmed datatypes. Currently, this must be turned on or off for the full metAMOS run.
Some advanced users may already have required programs installed (either in their path or non-standard location). INSTALL should check for these or allow the user to specify where the programs...
Future versions of metAMOS/iMetAMOS should include assembly polishing/improvement tools such as Pilon (http://www.broadinstitute.org/software/pilon/) or iCORN (http://icorn.sourceforge.net/).
Currently, the MapReads report only includes the contig coverage histogram. Include % reads mapped to contigs and % reads mapped between multiple contigs and maybe link histogram