Chromium De Novo Assembly
Supernova, printed on 08/17/2022
Release Notes for 1.1
- Fixes issue preventing mkfastq from demultiplexing data from recent sequencer software versions.
- Correctly handle extra commas in IEM samplesheets.
- Correctly handle absence of project folders.
- Correctly handle the second index in dual-indexed IEM samplesheets.
- Added instrumentation for diagnosing memory utilization issues.
- Added new metric for effective read coverage.
- Add auto-retry mechanism when pipeline stages fail due to causes that appear to be transient.
- --maxjobs now defaults to 64 in local jobmode.
- --jobinterval now defaults to 100ms in local jobmode.
- Fix for rare race condition in some Python components.
- Fixes issue preventing mkfastq from running bcl2fastq in certain circumstances.
Improved Assembly Quality
- Contigs are typically 10-20% longer.
- Corresponding records between the two pseudohap2 files now always share the same record number.
- Gap sizes are now estimated.
- Memory requirement reduced from 512GB to 384 GB.
- With 28 cores, assembles 1.2B human reads in 48 hours.
- New --localcores and --localmem options allow peak usage to be capped.
- Additional alerts to detect problematic run or sample conditions.
- Additional instrumentation to aid in debugging field issues.
New mkfastq Demultiplexing Pipeline
- Easier to integrate with existing bcl2fastq-based workflows.
- Now the preferred demultiplexing method, demux still available but deprecated.
- mkfastq is a thin wrapper around bcl2fastq with same basic interface.
- Accepts IEM-compatible stylesheets with added support for 10x sample index sets.
- Produces FASTQ files and folders in the same structure as bcl2fastq.
- Generates InterOp output for SAV.
- Also generates 10x-specific run QC metrics in JSON format.
- Pipestance output files (outs/) are no longer symlinks.
- Partial stage restart.
- Add output filename override, supports two output files having same basename.
- Add --onfinish handler support.
- Pipestances now generate a UUID in _uuid.