kpool's Introduction

Kpool

Overview

Kpool is a command-line utility which is part of a more general pipeline to identify sex-specific Kmers in pooled-sequencing data. Kpool implements two functions:

merging kmer tables from each pool into a common table (kmer tables are obtained with Jellyfish)
filtering this table for min/max frequencies in homogametic and heterogametic sex

Kpool was developed as part of a project by the LPGP lab from INRA, Rennes, France. It is still in beta and not officially released.

A more detailed README will be available soon.

Installation

# Clone the repository
git clone https://github.com/INRA-LPGP/kpool.git
# Navigate to the kpool directory
cd kpool
# Build kpool
make

Basic usage

Currently, Kpool has two commands:

merge: merge kmer tables from each pool into a common table (kmer tables are obtained with Jellyfish)
filter: filter a merged table based on kmer min/max frequencies in homogametic and heterogametic sex

Merge

kpool merge -m male_table -f female_table -o output_file

Options:

Flag	Type	Description
-m	`string`	Path to the male kmers table (output from Jellyfish)
-f	`string`	Path to the female kmers table (output from Jellyfish)
-o	`string`	Path to the output file (merged kmers table)

Filter

kpool filter -i merged_table -o output_file -s heterogametic_sex --min-het min_hetero_cov [ --max-het max_hetero_cov --max-hom max_homo_cov ]

Options:

Flag	Type	Description	Default
-i	`string`	Path to a merged kmers table
-o	`string`	Path to the ouput file (filter kmers table)
-s	`string`	Hetergogametic sex (M / F)
--min-het	`int`	Minimum kmer coverage in the heterogametic sex
--max-het	`int`	Maximum kmer coverage in the heterogametic sex	1000000
--max-hom	`int`	Maximum kmer coverage in the homogametic sex	0

Recommend Projects