If trimmomatic is not installed on your compter then the command 'dpkg -L trimmomatic' will give followin dpkg -L trimmomaticĭpkg-query: package 'trimmomatic' is not installed This will update the list of newest versions of packages and its dependencies on your system.Īfter downloading the latest package list with the help of above you can run the installation process. gzĪbove command will download the package lists for Ubuntu 17.04 on your system. Use of gzip format is determined based on the. It works with FASTQ (using phred + 33 or phred + 64 quality scores,ĭepending on the Illumina pipeline used), either uncompressed or * TOPHRED64: Convert quality scores to Phred-64
* TOPHRED33: Convert quality scores to Phred-33 * MINLENGTH: Drop the read if it is below a specified length * HEADCROP: Cut the specified number of bases from the start of the read * CROP: Cut the read to a specified length * TRAILING: Cut bases off the end of a read, if below a threshold quality * LEADING: Cut bases off the start of a read, if below a threshold quality * SLIDINGWINDOW: Perform a sliding window trimming, cutting once thesĪverage quality within the window falls below a threshold.
* ILLUMINACLIP: Cut adapter and other illumina-specific sequences from Their associated parameters are supplied on the command line. Paired-end and single ended data.The selection of trimming steps and Trimmomatic performs a variety of useful trimming tasks for illumina Flexible read trimming tool for Illumina NGS data
0 kommentar(er)
