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This article mainly explains "how to install and use Gerbil". Interested friends may wish to have a look at it. The method introduced in this paper is simple, fast and practical. Let's let the editor take you to learn how to install and use Gerbil.

For genome assembly, kmer count is one of the most basic analysis contents. Traditional kmer count tools have better performance when the length of kmer is less than 32, but for larger length kmer, the memory consumption and running speed are not satisfactory. With the continuous increase of sequencing read length, a tool that can support the counting of larger kmer and has good performance is very necessary.

Gerbil is such a tool that not only optimizes the algorithm, but also introduces GPU acceleration to further enhance its performance.

The following kmer count tools are listed in the literature

Jellyfish

BFCounter

DSK

KMC

Turtle

MSPKmerCounter

KCMBT

None of these tools performs as well as Gerbil for kmer with a length greater than 32. For the hg38 genome, the running speed of each software is as follows

As the length of kmer increases, the running time of Gerbil is always the fastest, where gGerbil represents the accelerated version of Gerbil of GPU.

The installation process is as follows

Git clone https://github.com/uni-halle/gerbil.gitcd gerbilmkdir buildcd buildcmake.. make

The basic usage is as follows

Gerbil-k 32 input.fasta temp_dir output_dir

The-k parameter specifies the length of kmer, where input.fasta represents the input sequence file, temp_dir represents the directory of temporary files, and output_dir represents the directory of output files.

Unlike jellysifh, Gerbil supports multiple input file formats

Fastq/fasta

Fastq.gz/fasta.gz

Fastq.bz2/fasta.bz2

Stdin

Txt

Support fastq and fasta formats, also support gzip and bzip two compressed formats, you can also read files from the standard input stream, or even a txt file, each line is a file path, so that you can process multiple input files at a time.

The output file of the software is a binary file, which can be converted to plain text format by toFasta command.

At this point, I believe you have a deeper understanding of "how to install and use Gerbil". You might as well do it in practice. Here is the website, more related content can enter the relevant channels to inquire, follow us, continue to learn!

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