Serghei Mangul edited this page Aug 3, 2018 · 9 revisions

Quick Start

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

  • for BAM file
./needle.sh toy.example.bam toy.example
  • or FASTQ file
./needle.sh -fastq toy.example.fastq toy.example

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

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