![]() Use of gzip format is determined based on the. * LEADING: Cut bases off the start of a read, if below a threshold quality * TRAILING: Cut bases off the end of a read, if below a threshold quality * CROP: Cut the read to a specified length * HEADCROP: Cut the specified number of bases from the start of the read * MINLENGTH: Drop the read if it is below a specified length * TOPHRED33: Convert quality scores to Phred-33 * TOPHRED64: Convert quality scores to Phred-64 It works with FASTQ (using phred + 33 or phred + 64 quality scores, depending on the Illumina pipeline used), either uncompressed or gzipp'ed FASTQ. A list of the other processing steps is presented in the Supplementary Materials. ![]() * SLIDINGWINDOW: Perform a sliding window trimming, cutting once thes average quality within the window falls below a threshold. Trimmomatic includes a variety of processing steps for read trimming and filtering, but the main algorithmic innovations are related to identification of adapter sequences and quality filtering, and are described in detail below. The current trimming steps are: * ILLUMINACLIP: Cut adapter and other illumina-specific sequences from the read. Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line. ![]()
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