NGS IgMatcher, Annotation Only - AbXtract

NGS for annotation and demultiplexing with IgMatcher.

Long-Read (PacBio) FILE Inputs
  • NGS Input FASTQ (Long-Read, E.G., PacBio) (file_in) : Input FASTQ File.
  • Barcode Table (Long-Read/PacBio IGMATCHER Cube), OPTIONAL (file_in) : Excel/CSV/TSV file containing barcodes with the column/comma/tab-separated format as “5’barcode,3’barcode,barcode_round,barcode_group”. Do not include header. If you only have a 5’ barcode then the column/comma/tab-separated format is “name, 5’barcode,,,”. If you just have a 3’ barcode then the column/comma/tab-separated format is “name,,3’barcode,,,”.
  • Species Database to Select From (Long-Read/PacBio IGMATCHER Cube) (string) : Species reference database to generate the db for igmatcher
    Default: [‘Human’]
    Choices: Alpaca, Human, Mouse, Rabbit
  • Provide a Customized DNA Database with Alignment Scheme of Interest (for NGS), OPTIONAL. (Long-Read/PacBio IGMATCHER Cube) (file_in) : ONLY REQUIRED for custom scaffolds like the Specifica Gen3 Library or codon optimized sequences: OPTIONAL for natural antibodies. If provided, will override annotation and species/database selection settings.
    1) match_name: name of the heavy or light chain scaffold. Examples include - mepolizumab_vh, mepolizumab_vl, IGHV1-18, IGLV1-36, IGKV1-12.
    2) Heavy chain representative should contain DNA bases space separated:
    match_name_vh FR1_dna CDR1_dna FR2_dna CDR2_dna FR3_dna CDR3_dna FR4_dna
    3) Light chain representative should contain DNA bases space separated:
    match_name_vl FR1_dna FR1_dna FR1_dna CDR2_dna FR3_dna CDR3_dna FR4_dna
    4) Each chain expected in sequence file needs least one representative (e.g., VH or VL).
    5) Each scaffold should contain at least one representative (e.g., Mepolizumab_VL, Mepolizumab_VH, IGHV1-18, IGLV1-36, IGKV1-12).

Short-Read (Illumina) FILE/SELECTION Inputs

  • NGS Input FASTQ Forward (Short-Read/Illumina) (file_in) : Path to FastQ containing Illumina sequences, read 1.
  • NGS Input FASTQ Reverse (Short-Read/Illumina) (file_in) : Path to FastQ containing Illumina sequences, read 2.
  • Barcode Table (Short-Read/Illumina IGMATCHER Cube), OPTIONAL (file_in) : Excel/CSV/TSV file containing barcodes with the column/comma/tab-separated format as “5’barcode,3’barcode,barcode_round,barcode_group”. Do not include header. If you only have a 5’ barcode then the column/comma/tab-separated format is “name, 5’barcode,,,”. If you just have a 3’ barcode then the column/comma/tab-separated format is “name,,3’barcode,,,”.
  • Species Database to Select From (Short-Read/Illumina IGMATCHER Cube) (string) : Species reference database to generate the db for igmatcher.
    Default: [‘Human’]
    Choices: Alpaca, Human, Mouse, Rabbit
  • Provide a Customized DNA Database with Alignment Scheme of Interest (for NGS), OPTIONAL. (Short-Read/NGS IGMATCHER Cube) (file_in) : ONLY REQUIRED for custom scaffolds like the Specifica Gen3 Library or codon optimized sequences: OPTIONAL for natural antibodies. If provided, will override annotation and species/database selection settings.
    1) match_name: name of the heavy or light chain scaffold. Examples include - mepolizumab_vh, mepolizumab_vl, IGHV1-18, IGLV1-36, IGKV1-12.
    2) Heavy chain representative should contain DNA bases space separated:
    match_name_vh FR1_dna CDR1_dna FR2_dna CDR2_dna FR3_dna CDR3_dna FR4_dna
    3) Light chain representative should contain DNA bases space separated:
    match_name_vl FR1_dna FR1_dna FR1_dna CDR2_dna FR3_dna CDR3_dna FR4_dna
    4) Each chain expected in sequence file needs least one representative (e.g., VH or VL).
    5) Each scaffold should contain at least one representative (e.g., Mepolizumab_VL, Mepolizumab_VH, IGHV1-18, IGLV1-36, IGKV1-12).