Bug fixes

• Fixes a bug where an upgrade to Illumina NovaSeq control software v1.8 (reagent name change in recipe XML file) resulted in a silent cellranger-arc mkfastq error and a significant number of reads going into Undetermined/ because the orientation of i5 (Index2) could not be autodetected

Bug fixes

• Fixes an issue where the metric "post-normalization number of reads" in the aggr web summary was incorrect.
• Fixes an issue where integer overflow could occur on large aggr or reanalyze runs.
• Fixes an issue where sample indices in the FASTQ header line were ignored unless the indices were reverse complemented.
• Fixes an issue where gex_umis_count in per_barcode_metrics.csv were all zeros.

New wavelet-based peak caller:

• Eliminates large peaks much larger than 5kb. Peaks have a tighter size distribution around ~ 1kb.
• Improves detection of cluster-specific peaks.
• Improves reproducibility between technical replicates.
• Consistent performance across a range of cell loads.
• Fixes crashes in the signal-background fitting procedure.

Changed the duplicate marking algorithm:

• Two read pairs are duplicates if they share the same start, end and cell barcode. Previously, only the start and end were used.
• Boosts median fragments per cell by as much as 25% at high cell loads.
• PCR and sequencer duplicates are no longer distinguished.

Improved computational performance:

• Up to 4x faster, 0.5x disk requirements.
• Complete rewrite of read processing and differential accessibility analysis in Rust.
• Minimize disk I/O.

Added the aggr pipeline to aggregate multiple libraries from multiple GEM wells.

Added the reanalyze pipeline to enable customized reanalysis.

Changed cell caller override: when --min-atac-count=X and --min-gex-count=Y is specified we choose all barcodes with atac count >= X and (previously or) gex count >= Y.

The raw feature barcode matrix now only contains barcodes with at least one ATAC count or one GEX count; previously, all allowed barcodes were present.

Change in barcode error correction: correct Hamming distance 1 errors (previously 2).

Added header lines beginning with # to the fragments.tsv.gz and peaks.bed files that contain version, reference and sample information.

Change to ATAC peak annotation TSV format:

• The peak column is now split into three columns: chrom, start, end.
• When a peak has multiple gene annotations, the same peak appears in multiple rows with each annotation. Previously, each row represented one peak and multiple annotations were expressed using ; separators in the same row.

Improvements to reference construction:

• Restrictions on the number of contigs or gene-containing contigs (primary contigs) in the reference have been eliminated.
• Bug fix for GTFs that do not contain a gene_name attribute.
• Contig names are allowed to contain - or _ characters.
• Eliminated discrepancies between reference checks in mkref and preflight checks in count. Previously, it was possible to pass checks in mkref and fail checks in count.

Eliminated secondary alignments from the position-sorted BAM.

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