# Using StrobeMap (C++)

## Installation

```
g++ -std=c++11 main.cpp index.cpp -o StrobeMap -O3 -mavx2
```

## Usage

```
 StrobeMap
strobealign [options] <references.fa> <queries.fasta>
options:
  -n INT number of strobes [2]
  -k INT strobe length, limited to 32 [20]
  -v strobe w_min offset [k+1]
  -w strobe w_max offset [70]
  -o name of output tsv-file [output.tsv]
  -c Choice of protocol to use; kmers, minstrobes, hybridstrobes, randstrobes [randstrobes]. 
```

EXAMPLE usage

```
# To create randstrobes (3,30,31,60)
StrobeMap -k 30 -n 3 -v 31 -w 60 -c randstrobes -o mapped.tsv  ref.fa query.fa
```
