NGS IgMatcher, Annotation Only - AbXtract

Category Paths

Follow one of these paths in the Orion user interface, to find the floe.

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

Barcode Table (barcode_table_ngs): File without header, formatted as Name,5’barcode,3’barcode,barcode_round,barcode_group If you just have a 5’ barcode write name,5’barcode,,, If you just have a 3’ barcode write name,,3’barcode,,,

Species Database to Select From (species_ngs): Species reference database to generate the db for igmatcher, must have value selected even if custom annotation file selected.

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.

Short-Read (Illumina) FILE Inputs

NGS Input FASTQ Forward (Short-Read/Illumina) (illumina_input_file1): Input FASTQ File 1

NGS Input FASTQ Reverse (Short-Read/Illumina) (illumina_input_file2): Input FASTQ File 2

Barcode Table (barcode_table_ngs_ill): File without header, formatted as Name,5’barcode,3’barcode,barcode_round,barcode_group If you just have a 5’ barcode write name,5’barcode,,, If you just have a 3’ barcode write name,,3’barcode,,,

Species Database to Select From (species_illumina): Species reference database to generate the db for igmatcher, must have value selected even if custom annotation file selected.

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.

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

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

Failure Output

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