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38 lines
1.6 KiB
Text
38 lines
1.6 KiB
Text
Trimmomatic: A flexible read trimming tool for Illumina NGS data
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Trimmomatic performs a variety of useful trimming tasks for illumina
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paired-end and single ended data.The selection of trimming steps and
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their associated parameters are supplied on the command line.
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The current trimming steps are:
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- ILLUMINACLIP: Cut adapter and other illumina-specific sequences from
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the read.
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- SLIDINGWINDOW: Perform a sliding window trimming, cutting once the
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average quality within the window falls below a threshold.
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- LEADING: Cut bases off the start of a read, if below a threshold
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quality
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- TRAILING: Cut bases off the end of a read, if below a threshold
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quality
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- CROP: Cut the read to a specified length
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- HEADCROP: Cut the specified number of bases from the start of the
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read
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- MINLEN: Drop the read if it is below a specified length
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- TOPHRED33: Convert quality scores to Phred-33
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- TOPHRED64: Convert quality scores to Phred-64
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It works with FASTQ (using phred + 33 or phred + 64 quality scores,
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depending on the Illumina pipeline used), either uncompressed or
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gzipp'ed FASTQ. Use of gzip format is determined based on the .gz
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extension.
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For single-ended data, one input and one output file are specified,
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plus the processing steps. For paired-end data, two input files are
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specified, and 4 output files, 2 for the 'paired' output where both
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reads survived the processing, and 2 for corresponding 'unpaired'
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output where a read survived, but the partner read did not.
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Citations
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Bolger, A. M., Lohse, M., & Usadel, B. (2014).
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Trimmomatic: A flexible trimmer for Illumina Sequence Data.
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Bioinformatics, btu170.
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