search

SyntekabioTools / HLAscan

Other
24 stars 2 forks source link

readme

HLAscan

Install with Bioconda

HLAscan Introduction

  1. Overview
    HLAscan is an alignment-based program that determines haplotypes taking read distribution into account. The software performs alignment of reads to HLA sequences from the international ImMunoGeneTics project/human leukocyte antigen (IMGT/HLA) database.
    The distribution of aligned reads was used to calculate a score function to determine correctly phased alleles by progressively removing false-positive alleles. HLAscan can be reliably applied for determination of HLA type across the whole-genome, exome, and target sequences.

  2. License terms
    HLAscan software is freely available for academic purposes and a license is required for commercial download and installation. Please contact service@syntekabio.com for questions regarding the license.

  3. Reference
    Ka, S., Lee, S., Hong, J., Cho, Y., ... & Jung, J. (2017). HLAscan: genotyping of the HLA region using next-generation sequencing data. BMC bioinformatics, 18(1), 258.

HLAscan_v2

  1. Updates
    (1) HLAscan v2 is compatible with human reference (hg19(v37) and v38).
    (2) Bam file and Fastq files can get to as an HLAscan v2 input.
    (3) Increase the ease of use.
    (4) Optimizations
    HLAscan v2 uses Suffix Array (SA) method instead of BWA-mem for alignment with IMGT/HLA Database.

    • Time efficiency : about 10 times faster than previous version (ex: under a minute for HLA-typing (<100dp))
    • Space efficiency : < 20MB disk (no create intermediate files)

  2. Contents
    (1) DB
    HLA-ALL.IMGT : IMGT/HLA database
    (2) Tool
    hla_scan_r_v2.1.4

  3. Usage
    (1) Download the DB & Tool
    (2) Read Manual

    ./hla_scan

    (3) Execute the tool

    • Bam Input 
      ./hla_scan –b [Bam file] –v [37/38] –d [DB] –g [Gene Symbol] –t [# of threads]
    • Fastq Input 
      ./hla_scan –l [fastq file] (-r [fastq file2]) –v [37/38] –d [DB] –g [Gene Symbol] –t [# of threads]

  4. Commands
    (1) HLA typing (input : bam file)

    ./hla_scan -b [bam] -d [IMGT/HLA DB] -v [version(37 or 38)]

    (2) HLA typing (input : fastq files)

    ./hla_scan -l [fastq] (-r [fastq2]) -d [IMGT/HLA DB]

  5. Options
    (1) Gene List -g [string], default=HLA-A

    HLA-A, HLA-B, HLA-C, HLA-E, HLA-F, HLA-G, MICA, MICB,
    HLA-DMA, HLA-DMB, HLA-DOA, HLA-DOB, HLA-DPA1, HLA-DPB1, HLA-DQA1,
    HLA-DQB1, HLA-DRA, HLA-DRB1, HLA-DRB5, TAP1, TAP2

    (2) Score Cutoff -s [int], default=50
    (3) Constant using ScoreFunc -c [int], default=30
    (4) # of threads -t [int], default=32

Download

You can download programs from the links underneath or from the release page

Dataset

You can download the dataset from here.