read_busco: Read and parse BUSCO's summary report

In almeidasilvaf/cogeqc: Systematic quality checks on comparative genomics analyses

Read and parse BUSCO's summary report

Description

Read and parse BUSCO's summary report

Usage

read_busco(result_dir = NULL)

Arguments

result_dir

Path to the directory where BUSCO results are stored. This function will look for the short_summary* file (single run) or short_summary* file (batch mode).

Value

A data frame with the following variables:

Class

BUSCO class. One of Complete_SC, Complete_duplicate, Fragmented, or Missing

Frequency

Frequency of BUSCOs in each class. If BUSCO was run in batch mode, this variable will contain relative frequencies. If BUSCO was run for a single file, it will contain absolute frequencies.

Lineage

Name of the lineage dataset used.

File (batch mode only)

Name of the input FASTA file.

Examples

result_dir <- system.file("extdata", package = "cogeqc")
df <- read_busco(result_dir)

almeidasilvaf/cogeqc documentation built on Jan. 29, 2024, 7:20 a.m.