Needle output details

Here we describe the output structure of Needle. The output consists of the following categories. Each category is reported separately for viruses, fungi, and protozoa.

Contigs assembled from candidate microbial reads

toy.example.fungi.megahit.contigs.fa     
toy.example.virus.megahit.contigs.fa
toy.example.protozoa.megahit.contigs.fa

• files with coverage information. One can use this file to plot the coverage plots

six directories corresponding to six steps of the ROP analysis of the unmapped reads. Additionally, it contains two directories corresponding to optional modules to characterize the mapped reads.

This is the typical output of the ROP pipelineewer

This is output for the toy example, which is distribuited with the tool.

toy.example.fungi.fastq
toy.example.fungi.megahit
toy.example.fungi.megahit.contigs.fa
toy.example.fungi.megahit.contigs.fa.amb
toy.example.fungi.megahit.contigs.fa.ann
toy.example.fungi.megahit.contigs.fa.bwt
toy.example.fungi.megahit.contigs.fa.pac
toy.example.fungi.megahit.contigs.fa.sa
toy.example.fungi.megahit.contigs.human.bam
toy.example.fungi.megahit.contigs.human.txt
toy.example.fungi.megahit.contigs.SV.bam
toy.example.megahit.contigs.fungi.bam
toy.example.megahit.contigs.fungi.cov
toy.example.megahit.contigs.fungi.uniq.cov
toy.example.megahit.contigs.protozoa.bam
toy.example.megahit.contigs.protozoa.cov
toy.example.megahit.contigs.protozoa.uniq.cov
toy.example.megahit.contigs.virus.bam
toy.example.megahit.contigs.virus.cov
toy.example.megahit.contigs.virus.uniq.cov
toy.example.protozoa.fastq
toy.example.protozoa.megahit
toy.example.protozoa.megahit.contigs.fa
toy.example.protozoa.megahit.contigs.fa.amb
toy.example.protozoa.megahit.contigs.fa.ann
toy.example.protozoa.megahit.contigs.fa.bwt
toy.example.protozoa.megahit.contigs.fa.pac
toy.example.protozoa.megahit.contigs.fa.sa
toy.example.protozoa.megahit.contigs.human.bam
toy.example.protozoa.megahit.contigs.human.txt
toy.example.protozoa.megahit.contigs.SV.bam
toy.example.unmapped.fastq
toy.example.virus.fastq
toy.example.virus.megahit
toy.example.virus.megahit.contigs.fa
toy.example.virus.megahit.contigs.fa.amb
toy.example.virus.megahit.contigs.fa.ann
toy.example.virus.megahit.contigs.fa.bwt
toy.example.virus.megahit.contigs.fa.pac
toy.example.virus.megahit.contigs.fa.sa
toy.example.virus.megahit.contigs.human.bam
toy.example.virus.megahit.contigs.human.txt
toy.example.virus.megahit.contigs.SV.bam