JCVI Genome Annotation

Description

JCVI Genome Annotation provides quantitative measures for the assessment of genome annotation.

The JCVI module parses the output of python -m jcvi.annotation.stats genestats <input.gff>. The file name is used as the sample name. If the output from the python -m jcvi.annotation.stats stats <input.gff> is present in the same directory, it is used to draw complementary plots.

A typical result directory will contain:

├── Exon_Count
│   ├── sample1.txt
│   └── sample2.txt
├── Exon_Length
│   ├── sample1.txt
│   └── sample2.txt
├── Gene_Length
│   ├── sample1.txt
│   └── sample2.txt
├── Intron_Length
│   ├── sample1.txt
│   └── sample2.txt
├── sample1_genestats.txt
└── sample2_genestats.txt

The JCVI module has been tested with output from JCVI v1.0.9.

File search patterns

jcvi:
  contents: "     o    % GC    % of genome    Average size (bp)    Median size
    (bp)    Number    Total length (Mb)"