danbing-tk

A toolkit for variable number tandem repeats (VNTRs) analysis, which enables:

1. building repeat-pan genome graphs for a set of "genotypable" VNTRs given haplotype-resolved assemblies (danbing-tk build),
2. genotyping each VNTR as a set of (k-mer, count) given short-read sequencing (SRS) data (danbing-tk align), and
3. predicting VNTR length from the genotype (danbing-tk predict).

Compiling source code

g++ -std=c++11 -O3 -lpthead danbing-tk.cpp

g++ -std=c++11 -O3 bam2pe.cpp

• repeat-pan genome graph databse

  ./kmers/pan.*.kmers are used by danbing-tk align

• sample usage

samtools fasta -@2 -n srs.bam |
awk '{if (substr($1,1,1) == ">") {
        if (substr($1,length($1)-1,1) == "/") { print substr($1, 1, length($1)-2) } else { print $1 } }
      else { print $1 }
     }' |
bam2pe -k 21 -fai /dev/stdin |
danbing-tk -gc 50 -k 21 -qs pan -fai /dev/stdin -o output_prefix -p 24 -cth 45 -rth 0.5

• Output format

>locus i
kmer0    kmer_count0
kmer1    kmer_count1
...
>locus i+1
...