trimmomatic
flexible read trimming tool for Illumina NGS data
Command lineScience
Not tested on a device yet. What that means
Commands in the package
TrimmomaticPETrimmomaticSE
About trimmomatic
From Debian's package description
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 thes 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
- 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. Use of gzip format is determined based on the .gz extension.
From Debian's description of the trimmomatic package, under that package's license.
Dependencies
Depends on
libjbzip2-javadefault-jre
Related apps
- sra-toolkitutilities for the NCBI Sequence Read ArchiveCommand line
- rsemRNA-Seq by Expectation-MaximizationCommand line
- dazzdbmanage nucleotide sequencing read dataCommand line
- trim-galoreautomate quality and adapter trimming for DNA sequencingCommand line
- deblurdeconvolution for Illumina amplicon sequencingCommand line
- atroposNGS read trimming tool that is specific, sensitive, and speedyCommand line
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the trimmomatic package, under that package's license.
- Description: Debian's description of the trimmomatic package, under that package's license.
- Versions and sizes: Debian's archive for ARM64, as on packages.debian.org.
- Popularity: Debian Popularity Contest counts.
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