BBDuk2 can operate in all 4 modes at once. “kmask=N” will, rather than trimming, convert all bases covered by reference kmers to N (or some other symbol). For ktrim=l, trimming will be done to the left instead. In ktrim=r mode, once a reference kmer is matched in a read, that kmer and all the bases to the right will be trimmed, leaving only the bases to the left this is the normal mode for adapter trimming. In order to kmer-trim, the flag “ktrim=r” or “ktrim=l” must be used. The default is filtering – any read matching a reference kmer will be discarded. If a reference is specified, BBDuk will operate on kmers in one of 4 modes: right-trimming, left-trimming, masking, or filtering. Pairs are always kept together – either both reads are kept, or both are discarded. When dealing with paired reads in 2 files they should always be processed together, not one at a time. BBDuk also supports input or output of paired reads in dual files using the in1, in2, out1, and out2 flags, for example:ībduk.sh in1=read1.fq in2=read2.fq out1=clean1.fq out2=clean2.fq The commands in this document assume either single-ended reads or paired reads in a single file. Paired reads interleaved in a single file will be autodetected based on their names this can be overridden with the “interleaved” flag. This file provides usage examples of various common tasks. BBDuk2 allows multiple kmer-based operations in a single pass, and is otherwise equivalent to BBDuk.īBDuk’s parameters are described in its shellscript (bbduk.sh).
Specifically, any combination of operations is possible in a single pass, with the exception of kmer-based operations (kmer trimming, kmer masking, or kmer filtering) at most 1 kmer-based operation can be done in a single pass. It is capable of quality-trimming and filtering, adapter-trimming, contaminant-filtering via kmer matching, sequence masking, GC-filtering, length filtering, entropy-filtering, format conversion, histogram generation, subsampling, quality-score recalibration, kmer cardinality estimation, and various other operations in a single pass. BBDuk was developed to combine most common data-quality-related trimming, filtering, and masking operations into a single high-performance tool. “Duk” stands for Decontamination Using Kmers.
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