mixcr buildLibrary

Build custom V/D/J/C gene segment library. See how to create custom library.

Command line options

mixcr buildLibrary 
    --species <species_name>
    --chain <chain>
    [--taxon-id <taxon_id>]
    (--v-genes-from-species <species> | [--v-genes-from-fasta <v.fasta> --v-gene-feature <gene_feature>])
    (--j-genes-from-species <species> | [--j-genes-from-fasta <j.fasta> [--j-gene-feature <gene_feature>]])
    [--d-genes-from-species <species> | [--d-genes-from-fasta <j.fasta> [--d-gene-feature <gene_feature>]]]
    [--c-genes-from-species <species> | [--c-genes-from-fasta <j.fasta> [--c-gene-feature <gene_feature>]]]
    [--do-not-infer-points]
    [--keep-intermediate]
    [--debug]
    [--force-overwrite]
    [--no-warnings]
    [--verbose]
    [--help]
    library.json[.gz]

--species <species_name>

Species name

--chain <chain>

Immunological chain

--v-genes-from-fasta <v.fasta>

FASTA file with Variable genes

--v-gene-feature <gene_feature>

Gene feature corresponding to Variable gene sequences in FASTA (e.g. VRegion or VGene)

--v-genes-from-species <species>

Species to take Variable genes from it (human, mmu, lamaGlama, alpaca, rat, spalax)

--j-genes-from-fasta <j.fasta>

FASTA file with Joining genes

--j-gene-feature <gene_feature>

Gene feature corresponding to Joining gene sequences in FASTA (JRegion by default)

--j-genes-from-species <species>

Species to take Joining genes from it (human, mmu, lamaGlama, alpaca, rat, spalax)

--d-genes-from-fasta <j.fasta>

FASTA file with Diversity genes

--d-gene-feature <gene_feature>

Gene feature corresponding to Diversity gene sequences in FASTA (DRegion by default)

--d-genes-from-species <species>

Species to take Diversity genes from it (human, mmu, lamaGlama, alpaca, rat, spalax)

--c-genes-from-fasta <j.fasta>

FASTA file with Constant genes

--c-gene-feature <gene_feature>

Gene feature corresponding to Constant gene sequences in FASTA (CExon1 by default)

--c-genes-from-species <species>

Species to take Constant genes from it (human, mmu, lamaGlama, alpaca, rat, spalax)

--taxon-id <taxon_id>

Taxon ID

--do-not-infer-points

Do not infer reference points

--keep-intermediate

Keep intermediate files

--debug

Print library debugging information

-f, --force-overwrite

Force overwrite of output file(s).

library.json[.gz]

Output library.