## ⚠️  Preset changes

- kAligner2 has been modified to work with both TCR and BCR data, the presets previously divided by the type of data now merged into one. Also, the division by `cdr3` and `full-length` presets has been deprecated; now the presets by default use the longest possible assembling feature according to the protocol:

- `qiaseq-human-tcr-cdr3` and `qiaseq-human-tcr-full-length` are deprecated and replaced by  `qiagen-human-rna-tcr-umi-qiaseq`. `qiagen-human-rna-tcr-umi-qiaseq` assemble clones by `{CDR2Begin:FR4End}` according to the manufactures read length recommendations.

- `qiaseq-mouse-tcr-cdr3` and `qiaseq-mouse-tcr-full-length` are deprecated and replaced by  `qiagen-mouse-rna-tcr-umi-qiaseq`. `qiagen-mouse-rna-tcr-umi-qiaseq` assemble clones by `{CDR2Begin:FR4End}` according to the manufactures read length recommendations.

- Parse bio preset `parse-bio-vdj-3gex` has been deprecated and raced by three presets according to the manufactures' kit options: `parsebio-sc-3gex-evercode-wt`, `parsebio-sc-3gex-evercode-wt-mini`, `parsebio-sc-3gex-evercode-wt-mega`. Now the presets include the whitelists for all CELL barcodes. CELL1, CELL2 and CELL3 now correspond to ParseBio Round 1, Round 2 and Round 3 (the order is reversed compared to the deprecated preset). Original Parse Bio cell barcodes naming has been added.

- Generic amplicon presets `generic-tcr-amplicon`, `generic-bcr-amplicon`, `generic-tcr-amplicon-umi` and `generic-bcr-amplicon-umi` are deprecated. New generic amplicon presets: `generic-amplicon` and `generic-amplicon-with-umi`

- `abhelix-human-bcr-cdr3`, `abhelix-human-bcr-full-length`, `abhelix-human-tcr-cdr3`, `abhelix-human-tcr-full-length` are all deprecated and replaced by `abhelix-human-rna-xcr` with the default assembling feature `{FR1Begin:FR4End}` according to the manufactures' protocol.

- `takara-human-bcr-cdr3` and `takara-human-bcr-full-length` are deprecated and replaced by `takara-human-rna-bcr-umi-smartseq` with assembling feature `{VDJRegion}`

- `takara-human-tcr-V2-cdr3` and `takara-human-tcr-V2-full-length` are deprecated and replaced by `takara-human-rna-tcr-umi-smarter-v2` with assembling feature `{VDJRegion}`

- `takara-human-tcr-V1-cdr3` and `takara-human-tcr-V1-full-length` are deprecated and replaced by `takara-human-rna-tcr-smarter` with assembling feature `{VDJRegion}`

- `takara-mouse-bcr-full-length` and `takara-mouse-tcr-cdr3` are deprecated and replaced by `takara-mouse-rna-bcr-smarter` with assembling feature `{VDJRegion}`

- `takara-mouse-tcr-cdr3` and `takara-mouse-tcr-full-length` are deprecated and replaced by `takara-mouse-rna-tcr-smarter` with assembling feature `{VDJRegion}`

- `biomed2-human-bcr-cdr3` and `biomed2-human-bcr-full-length` are deprecated and replaced by `biomed2-human-rna-igh` with assembling feature `{CDR1Begin:CDR3End}`

- `ampliseq-tcrb-sr-cdr3` has been deprecated and replaced with `illumina-human-rna-trb-ampliseq-sr`

- `ampliseq-tcrb-plus-full-length` and `ampliseq-tcrb-plus-cdr3` are deprecated and replaced by `illumina-human-rna-trb-ampliseq-plus` with assembling feature `{CDR1Begin:FR4End}`

- `irepertoire-human-rna-tcr-sr` and `irepertoire-human-rna-bcr-sr` are deprecated and replaced by `irepertoire-human-rna-xcr-repseq-sr`

- `irepertoire-human-rna-tcr-lr` and `irepertoire-human-rna-bcr-lr` are deprecated and replaced by `irepertoire-human-rna-xcr-repseq-lr`

- `irepertoire-mouse-rna-tcr-sr` and `irepertoire-mouse-rna-bcr-sr` are deprecated and replaced by `irepertoire-mouse-rna-xcr-repseq-sr`

- `irepertoire-mouse-rna-tcr-lr` and `irepertoire-mouse-rna-bcr-lr` are deprecated and replaced by `irepertoire-mouse-rna-xcr-repseq-lr`

- `irepertoire-human-dna-trb-sr` and `irepertoire-human-dna-igh-sr` are deprecated and replaced by `irepertoire-human-dna-xcr-repseq-sr`

- `irepertoire-human-dna-trb-lr` and `irepertoire-human-dna-igh-lr` are deprecated and replaced by `irepertoire-human-dna-xcr-repseq-lr`

- `milab-human-bcr-multiplex-cdr3` and `milab-human-bcr-multiplex-full-length` are deprecated and replaced by `milab-human-rna-ig-umi-multiplex` with assembling feature `{CDR1Begin:FR4End}`

- `milab-human-tcr-rna-race-full-length` and `milab-human-tcr-rna-race-cdr3` are deprecated and replaced by `milab-human-rna-tcr-umi-race` with assembling feature `{VDJRegion}`

- `milab-human-tcr-rna-multiplex-cdr3` is deprecated and replaced by `milab-human-rna-tcr-umi-multiplex`

- `milab-human-tcr-dna-multiplex-cdr3` is deprecated and replaced by `milab-human-dna-tcr-multiplex`

- `milab-mouse-tcr-rna-race-cdr3` and `milab-mouse-tcr-rna-race-full-length` are deprecated and replaced by `milab-mouse-rna-tcr-umi-race` with assembling feature `{VDJRegion}`

- `nebnext-human-bcr-cdr3`, `nebnext-human-bcr-full-length`, `nebnext-human-tcr-cdr3`, `nebnext-human-tcr-full-length`, `nebnext-human-tcr-bcr-full-length` and `nebnext-human-tcr-bcr-cdr3` are all deprecated and replaced by `neb-human-rna-xcr-umi-nebnext` with assembling feature `{VDJRegion}`

- `nebnext-mouse-bcr-cdr3`, `nebnext-mouse-bcr-full-length`, `nebnext-mouse-tcr-cdr3`, `nebnext-mouse-tcr-full-length`, `nebnext-mouse-tcr-bcr-full-length` and `nebnext-mouse-tcr-bcr-cdr3` are all deprecated and replaced by `neb-mouse-rna-xcr-umi-nebnext` with assembling feature `{VDJRegion}`

- `oncomine-human-tcrb-lr-cdr3` and `oncomine-human-tcrb-lr-full-length` are deprecated and replaced by `thermofisher-human-rna-trb-oncomine-lr` with assembling feature `{CDR1Begin:FR4End}`.

- `oncomine-human-tcrb-sr-cdr3` is deprecated and replaced by `thermofisher-human-rna-trb-oncomine-sr`.

- `oncomine-human-bcr-ihg-lr-cdr3` and `oncomine-human-bcr-ihg-lr-full-length` are deprecated and replaced by `thermofisher-human-rna-igh-oncomine-lr` with assembling feature `{CDR1Begin:FR4End}`.

- `oncomine-human-bcr-pan-clonality-cdr3` and `oncomine-human-tcr-pan-clonality-cdr3` are deprecated and replaced by `thermofisher-human-dna-bcr-oncomine-pan-clonality` and `thermofisher-human-dna-tcr-oncomine-pan-clonality`respectively.

- `oncomine-human-igh-fr3-j` is deprecated and replaced by `thermofisher-human-dna-igh-oncomine-fr3-j`.

- `oncomine-human-igh-fr2-j` is deprecated and replaced by `thermofisher-human-dna-igh-oncomine-fr2-j`.

- `oncomine-human-igh-fr1-j` is deprecated and replaced by `thermofisher-human-dna-igh-oncomine-fr1-j`.

- `oncomine-human-igh-leader-j` is deprecated and replaced by `thermofisher-human-dna-igh-oncomine-v-leader-j`.

- `10x-vdj-tcr`, `10x-vdj-tcr-full-length`, `10x-vdj-bcr` and `10x-vdj-bcr-full-length` are deprecated and replaced by `10x-sc-xcr-vdj`. By default, this preset assembles the longest possible contig for every clone, to replicate the `full-length` behavior one can use `--assemble-contigs-by VDJRegion` parameter to filter out the clones that do not cover the full VDJ region.

- `10x-5gex-cdr3` and `10x-5gex-full-length` are deprecated and replaced by `10x-sc-5gex`. By default, this preset assembles the longest possible contig for every clone, to replicate the `full-length` behavior one can use `--assemble-contigs-by VDJRegion` parameter to filter out the clones that do not cover the full VDJ region.

- `smartseq2-vdj-full-length` is deprecated and replaced by `smart-seq2-vdj`.

- `singleron-2.0.1-vdj-cdr3` is deprecated and replaced by `singleron-human-sc-xcr-gexscope-vdj`.

- `seqwell-vdj-cdr3` is deprecated and replaced by `seq-well-vdj`.

- `parse-bio-vdj-3gex` is deprecated. Three presets introduced according to vendor protocols: `parsebio-sc-3gex-evercode-wt`, `parsebio-sc-3gex-evercode-wt-mini`, `parsebio-sc-3gex-evercode-wt-mega`.

- `split-seq-vdj-3gex` is deprecated and replaced by `split-seq-3gex`.

- `ont-rna-seq-vdj-full-length` is deprecated and replaced by `ont-rna-seq`.

- New preset for FLAIRR-seq `flairr-seq-bcr`

- `bd-rhapsody-mouse-tcr-full-length`, `bd-rhapsody-mouse-bcr-full-length`, `bd-rhapsody-human-tcr-full-length` and `bd-rhapsody-human-bcr-full-length` are deprecated and replaced by `bd-sc-xcr-rhapsody-full-length`.

- `bd-rhapsody-human-tcr-v1`, `bd-rhapsody-human-bcr-v1`,`bd-rhapsody-human-tcr-v2`,`bd-rhapsody-human-bcr-v2` are now deprecated and replaced by `bd-human-sc-xcr-rhapsody-cdr3`

- `bd-rhapsody-mouse-tcr-v1`, `bd-rhapsody-mouse-bcr-v1`,`bd-rhapsody-mouse-tcr-v2`,`bd-rhapsody-mouse-bcr-v2` are now deprecated and replaced by `bd-mouse-sc-xcr-rhapsody-cdr3`

- All BD rhapsody presets now report CELLID number according to BD Rhapsoody.
