v4.4.0.suppl.md

⚠️ 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-clonalityrespectively.

• 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.