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Needle (full name: Needle in a haystack) combines alignment and assembly for comprehensive virome, mycobiome, and eukaryome 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 https://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 Needle output here