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Quick Start

Needle combines alignment and assembly for more comprehensive microbiome profiling on the strain level. Needle first identifies candidate microbial reads and assemble those into contigs. Mapping contigs onto the reference allow one to identify individual specific strains and corresponding structural variants.

Download needle

git clone git@github.com:smangul1/needle.git

Install needle and download necessary references

cd needle
./install.sh

Run needle by a single command

./needle.sh toy.example.bam toy.example

Find needle analysis in toy.example directory. Learn more about ROP output here