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Title:
seq2HLA - HLA typing from RNA-Seq sequence reads
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Release: 2.3
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Author:
Sebastian Boegel, 2012 - 2014 (c)
TRON - Translational Oncology at the University Medical Center Mainz, 55131 Mainz, Germany
University Medical Center of the Johannes Gutenberg-University Mainz, III. Medical Department, Mainz, Germany
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Contact:
boegels@uni-mainz.de
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Synopsis:
We developed an in-silico method "Seq2HLA", written in python and R, which takes standard RNA-Seq sequence reads in fastq format
as input, uses a bowtie index comprising all HLA alleles and outputs the most likely HLA class I and class II genotypes (in 4 digit resolution),
a p-value for each call, and the expression of each class
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Usage:
python seq2HLA.py -1 -2 -r "" [-p ]* [-3 ]**
*optional: number of parallel search threads for bowtie optional (Default:6)
**optional: trim int bases from the low-quality end of each read
readfile can be uncompressed or gzipped fastq file
runname should contain path information, e.g. "folder/subfolder/..../run", in order to store all resulting into to folder and all filenames will have the suffix run-
Output:
The results are output to stdout and to textfiles. Most important are:
i) -ClassI.HLAgenotype2digits => 2 digit result of Class I
ii) -ClassII.HLAgenotype2digits => 2 digit result of Class II
iii) -ClassI.HLAgenotype4digits => 4 digit result of Class I
iv) -ClassII.HLAgenotype4digits => 4 digit result of Class II
v) .ambiguity => reports typing ambuigities (more than one solution for an allele possible)
vi) -ClassI.expression => expression of Class I alleles
vii) -ClassII.expression => expression of Class II alleles
Dependencies:
0.) seq2HLA is a python script, developed with Python 2.6.8
1.) bowtie must be reachable by the command "bowtie". seq2HLA was developed and tested with bowtie version 0.12.7 (64-bit). The call to bowtie is invoked with 6 CPUs. You can change that by paramter -p.
2.) R must be installed, seq2HLA.py was developed and tested with R version 2.12.2 (2011-02-25)
3.) Input must be paired-end reads in fastq-format
4.) Index files must be located in the folder "references".
5.) Packages: biopython (developed with V1.58), numpy (1.3.0)
Version history:
2.3: typing of HLA II loci DRA, DPA1 and DPB1, typing of non-classical HLA I alleles (e.g. HLA-G...), cleaning up after execution (deletion of intermediate files) (August 2017)
2.2: improved performance, automatic detection of read length (option -l no longer required), user can choose number of parralel search threads (-p), seq2HLA now works with automatic path recognition, so it can be invoked from every path (April 2014)
2.1: supports gzipped fastq files as input
2.0: 4-digit typing
1.0: 2-digit typing
References:
Boegel, Sebastian; Loewer, Martin; Schaefer, Michael; Bukur, Thomas; Graaf, Jos de; Boisguerin, Valesca et al. (2013): HLA typing from RNA-Seq sequence reads. In: Genome Med 4 (12), S. 102. DOI: 10.1186/gm403.
Sebastian Boegel, Jelle Scholtalbers, Martin Löwer, Ugur Sahin, John C Castle (2015): In Silico HLA Typing Using Standard RNA-Seq Sequence Reads. In: Molecular Typing of Blood Cell Antigens
Sebastian Boegel, Martin Löwer, Thomas Bukur, Ugur Sahin, John C Castle (2014): A catalog of HLA type, HLA expression, and neo-epitope candidates in human cancer cell lines. In: OncoImmunology
Jelle Scholtalbers, Sebastian Boegel, Thomas Bukur, Marius Byl, Sebastian Goerges, Patrick Sorn, Martin Loewer, Ugur Sahin, John C Castle (2015): TCLP: an online cancer cell line catalogue integrating HLA type, predicted neo-epitopes, virus and gene expression. In: Genome Med
License:
The MIT License (MIT)
Copyright (c) 2012 Sebastian Boegel
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.
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