OptiType (version 1.3.5+galaxy0)

Single or Paired-end reads:

Select between paired and single end data

Select first set of reads:

Specify dataset with forward reads

Select second set of reads:

Specify dataset with reverse reads

Nucleotide Type:

homozygosity beta:

The beta value for for homozygosity detection (Leave blank for default: 0.009)

Enumerations:

The number of enumerations (Leave blank for default: 1)

ILP solver:

unpaired_weight:

In paired-end mode one might want to use reads with just one mapped end (e.g.,the other end falls outside the reference region). This setting allows theuser to keep them with an optionally reduced weight. A value of 0 means theyare discarded for typing, 0.2 means single reads are "worth" 20% of pairedreads, and a value of 1 means they are treated as valuable as properly mappedread pairs. Note: unpaired reads will be reported on the result coverage plotsfor completeness, regardless of this setting.

use_discordant:

We call a read pair discordant if its two ends best-map to two disjoint setsof alleles. Such reads can be either omitted or either of their ends treatedas unpaired hits. Note: discordant read pairs are reported on the coverageplots as unpaired reads, regardless of this setting.

OptiType

OptiType is a novel HLA genotyping algorithm based on integer linear programming, capable of producing accurate 4-digit HLA genotyping predictions from NGS data by simultaneously selecting all major and minor HLA Class I alleles.

INPUTS

RNA or DNA sequences in fastq format.

OUTPUTS

result.tsv A TAB-separated file of HLA genotyping predictions:
        A1      A2      B1      B2      C1      C2      Reads   Objective
0       A*31:01 A*68:01 B*40:01 B*51:01 C*15:02 C*03:04 132     128.43599999999998
coverage_plot.pdf Plots of coverage of HLA genotyping predictions