Type:DNA Fingerprinting

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Typing and Assembly

HISAT-genotype performs both typing and assembly for 13 DNA fingerprinting loci as follows.

Change the current directory to codis-analysis, where codis stands for Combined DNA Index System.

 hisat-genotype-top$ cd codis-analysis

After that you can perform CODIS typing and assembly for D13S317 locus on sequencing reads from a genome, NA12892 (Illumina's HiSeq 2000 platform).

 codis-analysis$ hisatgenotype_locus.py --base codis --locus-list D13S317 --num-editdist 2 -1 ILMN/NA12892.extracted.1.fq.gz -2 ILMN/NA12892.extracted.2.fq.gz

Internal Usage

 codis-analysis$ git clone https://github.com/infphilo/hisatgenotype_db
 codis-analysis$ hisat-genotype-top/hisatgenotype_modules/hisatgenotype_extract_codis_data.py
 (Manually fix some repeat structures in codis.dat)
 codis-analysis$ mv codis.dat hisatgenotype_db/CODIS/
 codis-analysis$ hisat-genotype-top/hisatgenotype_modules/hisatgenotype_convert_codis.py
 codis-analysis$ mv *_gen.fasta hisatgenotype_db/CODIS/fasta/;  mv *_gen.msf hisatgenotype_db/CODIS/msf/
 codis-analysis$ cd hisatgenotype_db; git commit -a -m "."; git push origin master; cd ..