10x Genomics
Chromium De Novo Assembly

Supernova, printed on 11/21/2024

Release Notes for 1.1

Supernova 1.1.5

• Fixes issue preventing mkfastq from demultiplexing data from recent sequencer software versions.

Supernova 1.1.4

mkfastq Improvements

• Correctly handle extra commas in IEM samplesheets.
• Correctly handle absence of project folders.
• Correctly handle the second index in dual-indexed IEM samplesheets.

Supernova 1.1.3

• Added instrumentation for diagnosing memory utilization issues.
• Added new metric for effective read coverage.

Supernova 1.1.2

• 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.

Supernova 1.1.1

• Fixes issue preventing mkfastq from running bcl2fastq in certain circumstances.

Supernova 1.1.0

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.

Resource Utilization

• 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.

Usability

• 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.

Martian Runtime

• 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.