Optikmer

Optikmer is a demonstration project for CSE 185 that estimates the k-mer length associated with the highest amount of distinct k-mers given one or more (filtered) fastq files. It is inspired by k-mer counting programs such as kmerGenie and jellyfish in terms of approximating the best k-mer length for de-novo assembly. See kmerGenie or jellyfish for more references.

Installation Instructions

Note: Installing and activating a virtual environment is highly recommended.

Once in your desired directory, optikmer can be installed with the following command:

pip install git+https://github.com/alicup29/Optikmer.git

If successfully installed, please refer to optikmer --help for further options.

Basic Usage

The basic usage of optikmer is:

optikmer [-k KMERS [KMERS ...]] [-o OUTPUT] filtered_read_1.fastq filtered_read_2.fasta ...

Note 1: If inputing compressed files (ex. fastq.gz and/or downloaded from NCBI), please uncompress with gunzip/zcat beforehand and use resulting fastq/fasta file.

Note 2: If specifying k-mer length(s), enter -k option FIRST, THEN -o to desired directory is required (. if current directory).

For example, the following command with analyze the fasta file ONLY with k=19, and output results to the current directory.

optikmer -k 19 -o . ~/Downloads/SRR28691205.fasta

Optikmer options

Optikmer requires at least one filtered/trimmed fastq file, optional User specifications are below.

• -k KMERS [KMERS ...], --kmers KMERS [KMERS ...]: User specifed k-mers to estimate, default is

[11, 21, 31, 41, 51, 61, 71, 81, 91]

• -o OUTPUT, --output OUTPUT: Write to output DIRECTORY, default written to current directory.

Example

1. Optikmer was installed and run with the following options:

• -k, --kmer: [19, 21]
• -o, --output (directory): results

1a. Open and activate virtual environment

1b. Install and check optikmer

1c. Ran with following command (dataset can be found in Optikmer/realdata/README.md)

2. All resulting files and images stored in ./results directory

3. Histogram report displays k-mer length with most unique k-mers at the top

Contributors

Project assembled by:

• Amick Licup (ID: A17038320)
• Annapurna Saladi (ID: A17417895)
• Steven Nguyen (ID: A16858016)