diff options
Diffstat (limited to 'academic/trimmomatic/README')
| -rw-r--r-- | academic/trimmomatic/README | 38 |
1 files changed, 38 insertions, 0 deletions
diff --git a/academic/trimmomatic/README b/academic/trimmomatic/README new file mode 100644 index 0000000000..339f90bdea --- /dev/null +++ b/academic/trimmomatic/README @@ -0,0 +1,38 @@ +Trimmomatic: A flexible read trimming tool for Illumina NGS data + +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. + +The current trimming steps are: + +- ILLUMINACLIP: Cut adapter and other illumina-specific sequences from + the read. +- SLIDINGWINDOW: Perform a sliding window trimming, cutting once the + average quality within the window falls below a threshold. +- 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 +- MINLEN: 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. Use of gzip format is determined based on the .gz +extension. + +For single-ended data, one input and one output file are specified, +plus the processing steps. For paired-end data, two input files are +specified, and 4 output files, 2 for the 'paired' output where both +reads survived the processing, and 2 for corresponding 'unpaired' +output where a read survived, but the partner read did not. + +Citations +Bolger, A. M., Lohse, M., & Usadel, B. (2014). +Trimmomatic: A flexible trimmer for Illumina Sequence Data. +Bioinformatics, btu170. |