v0.27.1

General

• [DEPRECATION] Support for split indices (with the -n option) will be deprecated in the next major release. It is now recommended to use --include-attribute and --exclude-attribute options, similar to Cellranger's mkref options (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references), to kb ref to reduce index size and memory usage.

ref

• A remote URL may be provided as the fasta (genomic FASTA) and/or gtf (gene annotation GTF) arguments. Support from ngs_tools 1.5.13.
• GTF is now allowed to have 0-length segments (pachterlab/kallisto#340).

count

• [DEPRECATION] Technology SMARTSEQ is now deprecated. All future uses should use BULK, SMARTSEQ2 or SMARTSEQ3.
• Genes that do not have a gene name will now have their gene IDs in the gene_name column (or the adata.var_names if --gene-names is used).
• Support for --workflow lamanno for -x BULK and -x SMARTSEQ2 technologies.