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.

Coverage files based only on uniquely mapped reads

toy.example.megahit.contigs.fungi.uniq.cov
toy.example.megahit.contigs.protozoa.uniq.cov
toy.example.megahit.contigs.virus.uniq.cov

Coverage from both uniqelly mapped reads and multi-mapped reads (e.g. reads mapped to multiple viral strains)

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

Microbial contigs mapped to microbial reference genomes

One can use this to infer differences between the donor contigs and microbial reference genomes. Such differences can correspond to structural variants

toy.example.fungi.megahit.contigs.SV.bam     
toy.example.virus.megahit.contigs.SV.bam
toy.example.protozoa.megahit.contigs.SV.bam

Typical output

This is output for the toy example, which is distributed 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

Additional files

Contigs which map to human. These contigs are filtered out

toy.example.fungi.megahit.contigs.human.txt
toy.example.protozoa.megahit.contigs.human.txt
toy.example.virus.megahit.contigs.human.txt