NGS IgMatcher, Annotation Only - AbXtract

Category Paths

  • Solution-based/Biologics/Antibody Design

  • Role-based/Bioinformatician

  • Role-based/Biologist

  • Product-based/AbXtract

Description

NGS for annotation and demultiplexing with IgMatcher.

Promoted Parameters

Title in user interface (promoted name)

Long-Read (PacBio) FILE Inputs

Long-Read (PacBio) NGS Input FASTQ (pacbio_input_file): Input FASTQ File

  • Type: file_in

Barcode Table (barcode_table_ngs): XLS/CSV/TSV file containing barcodes in the format Name,5’barcode,3’barcode,barcode_round(e.g., early/late),barcode_group Do not include header. If you just have a 5’ barcode write name,5’barcode,,, If you just have a 3’ barcode write name,,3’barcode,,,

  • Type: file_in

Species Database to Select From (species_ngs): Species reference database to generate the db for igmatcher

  • Required

  • Type: string

  • Default: [‘Human’]

  • Choices: [‘Alpaca’, ‘Human’, ‘Mouse’, ‘Rabbit’]

Provide a Customized DNA Annotation File with Alignment Scheme of Interest (for NGS). (custom_annotation_dna_igmatcher): 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.

  • Type: file_in

Short-Read (Illumina) FILE Inputs

NGS Input FASTQ Forward (Short-Read/Illumina) (illumina_input_file1): Input FASTQ File

  • Type: file_in

NGS Input FASTQ Reverse (Short-Read/Illumina) (illumina_input_file2): Input FASTQ File

  • Type: file_in

Barcode Table (barcode_table_ngs_ill): XLS/CSV/TSV file containing barcodes in the format Name,5’barcode,3’barcode,barcode_round(e.g., early/late),barcode_group Do not include header. If you just have a 5’ barcode write name,5’barcode,,, If you just have a 3’ barcode write name,,3’barcode,,,

  • Type: file_in

Species Database to Select From (species_illumina): Species reference database to generate the db for igmatcher

  • Required

  • Type: string

  • Default: [‘Human’]

  • Choices: [‘Alpaca’, ‘Human’, ‘Mouse’, ‘Rabbit’]

Provide a Customized DNA Annotation File with Alignment Scheme of Interest (for NGS). (custom_annotation_dna_igmatcher_illumina): 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.

  • Type: file_in

Upstream Long-Read (PacBio) AND/OR Short-Read (Illumina)

Output Basename of the Upstream Long-Read/PacBio Datasets (consolidate_out): This dataset contains all Long-Read/PacBio files processed immediately after IgMatcher

  • Required

  • Type: dataset_out

  • Default: up.long_read

Output Basename of the Upstream Short-Read/Illumina Datasets (consolidate_out_ill): This dataset contains all Short-Read/Illumina files processed immediately after IgMatcher

  • Required

  • Type: dataset_out

  • Default: up.short_read

Failure Output

Failed Dataset Output Name (fout): Contains failed records from both upstream and downstream processes

  • Required

  • Type: dataset_out

  • Default: problematic_ngs_annotation_only