HGSVC phase3 project repository (HHU)

Notes for revision

Following the update of the HG00514 Verkko assembly, only a subset of customized workflows was executed.

Updated:

# update of for SIG-MHC, extracted MHC region from new assembly
workflow::modules::regions::hla::extract.smk

# update of rDNA / ribotin runs, forwarded to Mir Henglin
workflow::modules::rdna::ribotin.smk

# update of alignment support for CHS trio (child HG00514)
workflow::modules::asm_compare::trio_align.smk

# update of HPRC gap evaluation
workflow::modules::regions::gaps::annotate_gaps.smk

The integrative QC analysis ("assembly label QC") was not updated because the complete run requires the annotation of centromeres, which is not available for HG00514 v2.

development notes / outdated

Verkko (env) updates

Last commit before updating MBG and GraphAligner to get bug fixes for last set of samples:

commit: #dbd3f7c88d9e28b052164c650e6ed56b7ba837de
  - graphaligner=1.0.17
  - mbg=1.0.15

Updated to

commit: #2fe632d38ea615fb93d1af63c462078490e285f9
  - graphaligner=1.0.18
  - mbg=1.0.16

for samples:

• YRI trio: NA19238, NA19239, NA19240
• CHS trio: HG00512, HG00513, HG00514
• HG00096
• HG00732 / PUR mother

Removed

NA19320 - cell line does not grow, insufficient ONT

Confirmed contamination

NA18939 HiFi - resequencing

Potential contamination

HG04036 HiFi - v1.4.1+dirty assembly completed NA21487 HiFi - v1.4.1+dirty assembly completed

Notes on Verkko

Production version currently is v1.4+dirty [added commits #3119b39 and #4f6a54e]

Notes on nomenclature

Trio kmer DBs

HXT - Illumina HiSeq X Ten NVS - Illumina NovaSeq (6000)