Generic presets:
generic-single-cell-gex (Generic single-cell gene expression)
  Required args:
    --species <name>

generic-ont (Oxford Nanopore data)
  Required args:
    --species <name>

generic-pacbio-with-umi (PacBio data with UMIs)
  Required args:
    --assemble-clonotypes-by <gene_features>
    --species <name>
    --tag-pattern <pattern>

generic-lt-single-cell-fragmented (Generic low throughput shotgun single-cell)
  Required args:
    --species <name>
    (--assemble-contigs-by <gene_features>|--assemble-contigs-by-cells)

generic-amplicon (Generic amplicon)
  Required args:
    (--floating-left-alignment-boundary [<anchor_point>]|--rigid-left-alignment-boundary [<anchor_point>])
    --assemble-clonotypes-by <gene_features>
    --species <name>
    (--floating-right-alignment-boundary (<gene_type>|<anchor_point>)|--rigid-right-alignment-boundary [(<gene_type>|<anchor_point>)])
    (--dna|--rna)

generic-ont-with-umi (Oxford Nanopore data with UMIs)
  Required args:
    --species <name>
    --tag-pattern <pattern>

generic-single-cell-gex-with-umi (Generic single-cell gene expression with UMIs)
  Required args:
    --species <name>
    --tag-pattern <pattern>

generic-ht-single-cell-fragmented-with-umi (Generic high throughput shotgun single-cell with UMIs)
  Required args:
    --species <name>
    (--assemble-contigs-by <gene_features>|--assemble-contigs-by-cells)
    --tag-pattern <pattern>

smart-seq2-vdj (Smart-Seq2)
  Required args:
    --species <name>

generic-lt-single-cell-amplicon-with-umi (Generic low throughput amplicon single-cell with UMIs)
  Required args:
    (--floating-left-alignment-boundary [<anchor_point>]|--rigid-left-alignment-boundary [<anchor_point>])
    --assemble-clonotypes-by <gene_features>
    --species <name>
    (--floating-right-alignment-boundary (<gene_type>|<anchor_point>)|--rigid-right-alignment-boundary [(<gene_type>|<anchor_point>)])

generic-amplicon-with-umi (Generic amplicon with UMI barcodes)
  Required args:
    (--floating-left-alignment-boundary [<anchor_point>]|--rigid-left-alignment-boundary [<anchor_point>])
    --assemble-clonotypes-by <gene_features>
    --species <name>
    (--floating-right-alignment-boundary (<gene_type>|<anchor_point>)|--rigid-right-alignment-boundary [(<gene_type>|<anchor_point>)])
    (--dna|--rna)
    --tag-pattern <pattern>

generic-ht-single-cell-fragmented (Generic high throughput shotgun single-cell)
  Required args:
    --species <name>
    (--assemble-contigs-by <gene_features>|--assemble-contigs-by-cells)
    --tag-pattern <pattern>

generic-lt-single-cell-amplicon (Generic low throughput amplicon single-cell)
  Required args:
    (--floating-left-alignment-boundary [<anchor_point>]|--rigid-left-alignment-boundary [<anchor_point>])
    --assemble-clonotypes-by <gene_features>
    --species <name>
    (--floating-right-alignment-boundary (<gene_type>|<anchor_point>)|--rigid-right-alignment-boundary [(<gene_type>|<anchor_point>)])

generic-ht-single-cell-amplicon-with-umi (Generic high throughput amplicon single-cell with UMIs)
  Required args:
    (--floating-left-alignment-boundary [<anchor_point>]|--rigid-left-alignment-boundary [<anchor_point>])
    --assemble-clonotypes-by <gene_features>
    --species <name>
    (--floating-right-alignment-boundary (<gene_type>|<anchor_point>)|--rigid-right-alignment-boundary [(<gene_type>|<anchor_point>)])
    --tag-pattern <pattern>

generic-pacbio (PacBio data)
  Required args:
    --assemble-clonotypes-by <gene_features>
    --species <name>

rna-seq (RNA-Seq data)
  Required args:
    --species <name>

exome-seq (Exome-Seq data)
  Required args:
    --species <name>

generic-ht-single-cell-amplicon (Generic high throughput amplicon single-cell)
  Required args:
    (--floating-left-alignment-boundary [<anchor_point>]|--rigid-left-alignment-boundary [<anchor_point>])
    --assemble-clonotypes-by <gene_features>
    --species <name>
    (--floating-right-alignment-boundary (<gene_type>|<anchor_point>)|--rigid-right-alignment-boundary [(<gene_type>|<anchor_point>)])
    --tag-pattern <pattern>

generic-lt-single-cell-fragmented-with-umi (Generic low throughput shotgun single-cell with UMIs)
  Required args:
    --species <name>
    (--assemble-contigs-by <gene_features>|--assemble-contigs-by-cells)

-----Invivoscribe-----
invivoscribe-human-dna-igk-lymphotrack (LymphoTrack IGK Assay Panel)

invivoscribe-human-dna-igh-fr2-lymphotrack (LymphoTrack IGH FR2)

invivoscribe-human-dna-igh-fr123-lymphotrack (LymphoTrack IGH FR1/2/3)

invivoscribe-human-dna-ighv-leader-lymphotrack (LymphoTrack IGHV Leader Somatic Hypermutation)

invivoscribe-human-dna-igh-fr1-lymphotrack (LymphoTrack IGH FR1)

invivoscribe-human-dna-igh-fr3-lymphotrack (LymphoTrack IGH FR3)

invivoscribe-human-dna-trb-lymphotrack (LymphoTrack TRB Assay Panel)

invivoscribe-human-dna-trg-lymphotrack (LymphoTrack TRG Assay Panel)

-----Cellecta-----
cellecta-mouse-rna-xcr-umi-drivermap-air (DriverMap Adaptive Immune Receptor (AIR) TCR-BCR Profiling Mouse RNA)

cellecta-human-rna-xcr-umi-drivermap-air-bcr-spikein-16-4-1 (DriverMap Adaptive Immune Receptor (AIR) TCR-BCR Profiling Human RNA with BCR Spike-in mix 16:4:1)

cellecta-human-rna-xcr-full-length-umi-drivermap-air (DriverMap Adaptive Immune Receptor (AIR) Full-length TCR-BCR Profiling Human RNA)

cellecta-human-dna-xcr-umi-drivermap-air (DriverMap Adaptive Immune Receptor (AIR) TCR-BCR Profiling Human DNA)

cellecta-human-rna-xcr-umi-drivermap-air-tcr-spikein-16-4-1 (DriverMap Adaptive Immune Receptor (AIR) TCR-BCR Profiling Human RNA with TCR Spike-in mix 16:4:1)

cellecta-human-rna-xcr-umi-drivermap-air-bcr-spikein-1-1-1 (DriverMap Adaptive Immune Receptor (AIR) TCR-BCR Profiling Human RNA with BCR Spike-in mix 1:1:1)

cellecta-human-rna-xcr-umi-drivermap-air-tcr-spikein-1-1-1 (DriverMap Adaptive Immune Receptor (AIR) TCR-BCR Profiling Human RNA with TCR Spike-in mix 1:1:1)

cellecta-human-rna-xcr-umi-drivermap-air (DriverMap Adaptive Immune Receptor (AIR) TCR-BCR Profiling)

-----Thermo Fisher-----
thermofisher-mouse-dna-igh-ampliseq-sr (Ion AmpliSeq Mouse IGH‑SR DNA)

thermofisher-human-dna-igh-oncomine-sr (Oncomine DNA IGH SR Assay)

thermofisher-mouse-rna-tcb-ampliseq-sr (Ion AmpliSeq Mouse TCR Beta‑SR RNA)

thermofisher-human-dna-trb-oncomine-sr (Oncomine DNA TCR Beta‑LR Assay)

thermofisher-human-dna-bcr-oncomine-pan-clonality (Oncomine BCR Pan-Clonality Assay)

thermofisher-human-dna-igh-oncomine-v-leader-j (Oncomine IGH Leader-J Assay)

thermofisher-human-dna-igh-oncomine-fr1-j (Oncomine IGH FR1-J Assay)

thermofisher-human-rna-igh-oncomine-lr (Oncomine RNA IGH LR Assay)

thermofisher-human-dna-tcr-oncomine-pan-clonality (Oncomine TCR Pan-Clonality Assay)

thermofisher-human-rna-igh-oncomine-sr (Oncomine RNA IGH SR Assay)

thermofisher-human-dna-igh-oncomine-fr3-j (Oncomine IGH FR3(d)-J Assay)

thermofisher-human-rna-trb-oncomine-sr (Oncomine RNA TCR Beta‑SR Assay)

thermofisher-mouse-dna-tcb-ampliseq-sr (Ion AmpliSeq Mouse TCR Beta‑SR DNA)

thermofisher-mouse-rna-igh-ampliseq-sr (Ion AmpliSeq Mouse IGH‑SR RNA)

thermofisher-human-rna-trb-oncomine-lr (Oncomine RNA TCR Beta‑LR Assay)

thermofisher-human-dna-igh-oncomine-fr2-j (Oncomine IGH FR2-J Assay)

-----iRepertoire-----
irepertoire-human-dna-xcr-repseq-sr (Human DNA IGH/TCR Repseq Short Read)

irepertoire-mouse-rna-xcr-repseq-lr (Mouse IGH/TCR Repseq Long Read)

irepertoire-human-dna-xcr-repseq-lr (Human DNA IGH/TCR Repseq Long Read)

irepertoire-mouse-rna-xcr-repseq-sr (Mouse IGH/TCR Repseq Short Read)

irepertoire-mouse-rna-xcr-repseq-plus (Mouse IGH/TCR Repseq Plus)

irepertoire-mouse-rna-xcr-repseq-plus-umi-pe (Mouse IGH/TCR Repseq Plus with UMI Paired End)

irepertoire-human-rna-xcr-repseq-plus-umi-pe (Human IGH/TCR Repseq Plus with UMI Paired End)

irepertoire-human-rna-xcr-repseq-plus-umi-se (Human IGH/TCR Repseq Plus with UMI Single End)

irepertoire-human-rna-xcr-repseq-sr (Human IGH/TCR Repseq Short Read)

irepertoire-human-rna-xcr-repseq-plus (Human IGH/TCR Repseq Plus)

irepertoire-human-rna-xcr-repseq-lr (Human IGH/TCR Repseq Long Read)

-----Takara Bio-----
takara-human-rna-tcr-umi-smarter-v2 (SMARTer Human TCR a/b Profiling Kit v2)

takara-sc-human-rna-tcr-smarter (SMARTer Human scTCR a/b Profiling Kit)

takara-mouse-rna-tcr-smarter (SMARTer Mouse TCR a/b Profiling Kit)

takara-mouse-rna-tcr-umi-smarseq (SMART-Seq Mouse TCR (with UMIs))

takara-human-rna-tcr-umi-smartseq (SMART-Seq Human TCR (with UMIs))

takara-mouse-rna-bcr-smarter (SMARTer Mouse BCR IgG H/K/L Profiling Kit)

takara-human-rna-bcr-umi-smarter (SMARTer Human BCR IgG IgM H/K/L Profiling Kit)

takara-human-rna-tcr-smarter (SMARTer Human TCR a/b Profiling Kit)

takara-mouse-rna-bcr-umi-smarseq (SMART-Seq Mouse BCR (with UMIs))

takara-human-rna-bcr-umi-smartseq (SMART-Seq Human BCR (with UMIs))

-----MiLaboratories-----
milab-human-rna-tcr-umi-multiplex (Human TCR RNA Multiplex)

milab-mouse-rna-tcr-umi-race (Mouse TCR RNA 5'RACE)

milab-human-rna-tcr-umi-race (Human TCR RNA 5'RACE)

milab-human-dna-xcr-7genes-multiplex (Human 7GENES DNA Multiplex)

milab-human-dna-tcr-multiplex (Human TCR DNA Multiplex)

milab-human-rna-ig-umi-multiplex (Human Ig RNA Multiplex)

-----Integrated DNA Technologies-----
idt-human-rna-tcr-umi-archer (Archer IMMUNOVerse TCR panel)
  Required args:
    --assemble-clonotypes-by <gene_features>

idt-human-rna-bcr-umi-archer (Archer IMMUNOVerse BCR panel)

-----Illumina-----
illumina-human-rna-trb-ampliseq-plus (Human TCR Beta Ampliseq Plus)

illumina-human-rna-trb-ampliseq-sr (Human TCR Beta RNA Ampliseq Short Read)

illumina-human-dna-trb-ampliseq-sr (Human TCR Beta DNA Ampliseq Short Read)

-----Public-----
vergani-et-al-2017-full-length (Vergani et al., 2017)

seq-well-vdj (Seq-well VDJ)
  Required args:
    --species <name>
    --assemble-clonotypes-by <gene_features>

mikelov-et-al-2021 (Mikelov et al., 2021)

split-seq-3gex (SPLIT-seq 3' Gene expression)
  Required args:
    --species <name>

biomed2-human-rna-igkl (BIOMED2 IGK/IGL)

vergani-et-al-2017-cdr3 (Vergani et al., 2017)

han-et-al-2014 (Han et al., 2014)
  Required args:
    --species <name>

flairr-seq-bcr (FLLAIRR-seq)

biomed2-human-rna-igh (BIOMED2 IGH)

biomed2-human-rna-trbdg (BIOMED2 TCR Beta/Delta/Gamma)

-----Parse Biosciences-----
parsebio-sc-3gex-evercode-wt (Evercode single-cell WT)
  Required args:
    --species <name>

parsebio-sc-3gex-evercode-wt-mini (Evercode single-cell WT Mini)
  Required args:
    --species <name>

parsebio-sc-3gex-evercode-wt-mega (Evercode single-cell WT Mega)
  Required args:
    --species <name>

-----BD biosciences-----
bd-mouse-sc-xcr-rhapsody-cdr3 (Rhapsody Mouse VDJ CDR3 Assay)

bd-sc-xcr-rhapsody-full-length (Rhapsody Full-length TCR/BCR Multiomic Assay)
  Required args:
    --species <name>

bd-sc-xcr-rhapsody-full-length-enhanced-bead-v2 (Rhapsody Full-length TCR/BCR Multiomic Assay Enhaced Beads V2)
  Required args:
    --species <name>

bd-human-sc-xcr-rhapsody-cdr3 (Rhapsody Human VDJ CDR3 Assay)

-----QIAGEN-----
qiagen-human-rna-tcr-umi-qiaseq (QIAseq Human TCR Panel Immune Repertoire RNA Library Kit)

qiagen-mouse-rna-tcr-umi-targeted-qiaseq (QIAseq Targeted RNA Panel Mouse TCR)

qiagen-mouse-rna-tcr-umi-qiaseq (QIAseq Mouse TCR Panel Immune Repertoire RNA Library Kit)

qiagen-human-rna-tcr-umi-targeted-qiaseq (QIAseq Targeted RNA Panel Human TCR)

-----New England BioLabs-----
neb-human-rna-xcr-umi-nebnext (NEBNext® Immune Sequencing Kit (Human) BCR & TCR)

neb-mouse-rna-xcr-umi-nebnext (NEBNext® Immune Sequencing Kit (Mouse) BCR & TCR)

-----10x Genomics-----
10x-sc-5gex (5' Single cell gene expression)
  Required args:
    --species <name>

10x-sc-xcr-vdj (5' Single cell VDJ)
  Required args:
    --species <name>

-----Bruker-----
bruker-human-sc-xcr-vdj-beacon (Single cell VDJ)

-----AbHelix-----
abhelix-human-rna-xcr (Human immunoglobulin repertoire)

-----Singleron Biotechnologies-----
singleron-human-sc-xcr-gexscope-vdj (GEXSCOPE Human Single Cell V(D)J Kit )
  Required args:
    --assemble-clonotypes-by <gene_features>

