Quick Sanger from ABI Traces - AbXtract¶
Category Paths
Follow one of these paths in the Orion user interface, to find the floe.
Solution-based/Biologics/Antibody Design
Role-based/Bioinformatician
Role-based/Biologist
Product-based/AbXtract
Description
This will process paired or unpaired ab1 files. Each sequence ID typically represents unique well ID. This will condense AA sequences based on user-defined option (Default = Full-Length, Framework included). Redundant sequences will be condensed and the ‘id’ field will contain a ‘:’ separated list of IDs (typically Well ID). This FLOE will calculate liabilities and biophysical properties by CDR (length, net charge, Parker hydropathy).
Promoted Parameters
Title in user interface (promoted name)
Trace Assembly and Contig Trimming Parameters
Read trimming stringency (trim_stringency): Stringency of read trimming prior to assembly. If value is 0, floe ignores this parameter and trims by length (see ASSEMBLE TRACES Cube hidden parameters to set lengths).To enable this parameter, choose an integer between 1-9. 1 is the most stringent and 9 is the least stringent. Incompletely trimmed reads may result in insertions in the assembled sequence but too much trimming may remove clone start and end sites.
Required
Type: integer
Default: 5
Name of forward primer (for_primer_name): Used to parse forward reads (read 1) from ab1 files by name. Primer should be the last part of the file name, e.g., Clone1-PrimerF.ab1. Click the + to add additional forward primer names. Recommended: include the delimiter (e.g., ‘-‘) preceding the primer name to ensure it is removed from the clone ID in the output dataset.
Type: string
Default: []
Name of reverse primer (rev_primer_name): Used to parse reverse reads (read 2) from ab1 files by name. Primer should be the last part of the file name, e.g., Clone1-PrimerR.ab1.Click the + to add additional reverse primer names. Recommended: include the delimiter (e.g., ‘-‘) preceding the primer name to ensure it is removed from the clone ID in the output dataset.
Type: string
Default: []
Trim # nucleotides from 3-prime end of read (trim_length_up): Trim # nucleotides from 3-prime end of assembled read to remove primer and/or extraneous sequence prior to annotation.
Type: integer
Default: 0
Trim nucleotides upstream of this sequence (trim_bases_up): Trim nucleotides upstream of this sequence to remove primer and/or extraneous sequence after assembly and prior to annotation. Identifies first instance of this sequence.
Type: string
Default:
Upstream sequence mismatches (mismatches_up): Number of substitutions to allow in upstream sequence match.
Type: integer
Default: 1
Trim # nucleotides from 5-prime end of read (trim_length_down): Trim # nucleotides from 5- end of assembled read to remove primer and/or extraneous sequence prior to annotation.
Type: integer
Default: 0
Trim nucleotides downstream of this sequence (trim_bases_down): Trim nucleotides downstream of this sequence to remove primer and/or extraneous sequence after assembly and prior to annotation. Identifies last instance of this sequence.
Type: string
Default:
Downstream sequence mismatches (mismatches_down): Number of substitutions to allow in downstream sequence match.
Type: integer
Default: 1
Key Liability Parameters
Polyspecificity Liabilities (liability_choices_poly): polyspecificity liabilities to quantify
Type: string
Default: [‘Three Consecutive Aromatics - Polyspecificity’, ‘RR - Polyspecificity’, ‘VG - Polyspecificity’, ‘VV - Polyspecificity’, ‘WW - Polyspecificity’, ‘GGG - Polyspecificity’, ‘WXW - Polyspecificity’, ‘YY - Polyspecificity’]
Choices: [‘Three Consecutive Aromatics - Polyspecificity’, ‘RR - Polyspecificity’, ‘VG - Polyspecificity’, ‘VV - Polyspecificity’, ‘YY - Polyspecificity’, ‘WW - Polyspecificity’, ‘GGG - Polyspecificity’, ‘WXW - Polyspecificity’]
Deamidation Liabilities (liability_choices_deam): deamidation liabilities to quantify
Type: string
Default: [‘NG - Deamidation’, ‘NS - Deamidation’, ‘NT - Deamidation’, ‘NN - Deamidation’, ‘GNF - Deamidation’, ‘GNY - Deamidation’, ‘GNT - Deamidation’, ‘GNG - Deamidation’, ‘QG - Glutamine Deamidation’]
Choices: [‘N[GSTN] - Deamidation’, ‘NG - Deamidation’, ‘NS - Deamidation’, ‘NT - Deamidation’, ‘NN - Deamidation’, ‘GN[FYTG] - Deamidation’, ‘GNF - Deamidation’, ‘GNY - Deamidation’, ‘GNT - Deamidation’, ‘GNG - Deamidation’, ‘QG - Glutamine Deamidation’]
Glycosylation Liabilities (liability_choices_glyc): glycosylation liabilities to quantify
Type: string
Default: [‘NXT/S - Glycosylation’]
Choices: [‘NXT/S - Glycosylation’, ‘NXT - Glycosylation’, ‘NXS - Glycosylation’]
Hydrolysis Liabilities (liability_choices_hydrolysis): hydrolysis liabilities to quantify
Type: string
Default: [‘DP - Hydrolysis’]
Choices: [‘DP - Hydrolysis’]
Isomerization Liabilities (liability_choices_iso): isomerization liabilities to quantify
Type: string
Default: [‘DG - Isomerization’, ‘DS - Isomerization’, ‘DD - Isomerization’]
Choices: [‘D[GSD] - Isomerization’, ‘DG - Isomerization’, ‘DS - Isomerization’, ‘DD - Isomerization’]
Biophysical Liabilities (liability_choices_charge): Net charge or hydropathy liabilities to quantify
Type: string
Default: [‘Charge (>1)’]
Choices: [‘Charge (>-1)’, ‘Charge (>0)’, ‘Charge (>1)’, ‘Charge (>2)’, ‘Charge (>3)’, ‘Charge (>4)’, ‘Parker Hydropathy (<0.0)’, ‘Parker Hydropathy (<-0.1)’, ‘Parker Hydropathy (<-0.2)’, ‘Parker Hydropathy (<-0.3)’, ‘Parker Hydropathy (<-0.4)’, ‘Parker Hydropathy (<-0.5)’, ‘Parker Hydropathy (<-0.6)’, ‘Parker Hydropathy (<-0.7)’, ‘Parker Hydropathy (<-0.8)’, ‘Parker Hydropathy (<-0.9)’, ‘Parker Hydropathy (<-1.0)’, ‘Parker Hydropathy (<-2.0)’, ‘Parker Hydropathy (<-3.0)’, ‘Parker Hydropathy (<-4.0)’, ‘Parker Hydropathy (<-5.0)’]
Cysteine Liabilities (liability_choices_cysteine): cysteine-based liabilities to quantify
Type: string
Default: [‘Unpaired Cysteine’]
Choices: [‘Unpaired Cysteine’, ‘Any Cysteine’]
Process by Population Parameters (OPTIONAL)
Write Populations to Their Own Dataset After Processing (Quick Sanger Field Consolidation Cube) (write_group): Set this ON to split a single input file by population when analyzing. Data will be written to separate upstream datasets but a single consolidated downstream dataset.
Required
Type: boolean
Default: False
Choices: [True, False]
Clone name delimiter (delimiter): Use this delimiter to identify population from clone name
Type: string
Default: _
First part of clone name defining population (population_start): Use a 1-indexed integer to indicate start of population name after splitting on delimiter
Type: integer
Default: 1
Last part of clone name defining population (population_end): Use a 1-indexed integer to indicate end of population name after splitting on delimiter
Type: integer
Default: -1
Key Clustering Parameters
Clustering Type (cluster_type): Cluster type to apply to sequencing dataset
Required
Type: string
Default: Unique Only
Choices: [‘AbScan’, ‘Unique Only’, ‘Levenshtein Distance’, ‘Hamming Distance’]
Max Distance for Levenshtein or Hamming, If Selected (max_dist_ld_hm): Select the maximum edit distance for two sequences to belong to same cluster group (must be >= 1 to take effect). Works if Levenshtein Distance or Hamming Distance selected for Clustering Type. See Hidden Parameters for AbScan (though do not recommend Abscan for N<=200)
Required
Type: integer
Default: 0
Region of Interest For Clustering Sanger Sequences (Uses Clustering Type Parameter) (roi_cluster): Indicate the region of interest for processing, only top representative full-length sequence will be kept. IF INPUT IS ILLUMINA WILL ONLY USE CDR3 (CHAIN_1/UPSTREAM CHAIN) CLUSTERING.
Required
Type: string
Default: CDR3 Chain_2 (Downstream Chain)
Choices: [‘Merged CDRs’, ‘CDR3 Chain_1 (Upstream Chain)’, ‘CDR3 Chain_2 (Downstream Chain)’, ‘HCDR3 and LCDR3’, ‘Full-Length’]