Edit distance creates even more kmers, at 1+(8*k)^edist. So, for E.coli with K=31 and hdist=0, there are 4554207 kmers stored, using around 140MB, taking about 0.5 seconds with hdist=1, there are 427998710 kmers stored (94 times as many), using 15GB, and taking 104 seconds. If a hamming distance is used, such as hdist=1, then the number of kmers stored will be multiplied by 1+(3*k)^hdist. Kmers, hdist, qhdist, and edist:Р”Р„ 4.6Mbp genome like E.coli contains around 4.6 million unique kmers. The actual maximum you can use depends on the operating systemРІР‚в„ўs configuration. If you will using a large reference, modify that flag to be around 85% of the machineРІР‚в„ўs physical memory РІР‚вЂњ for example, -Xmx27g on a 32GB machine. So, if you are not going to be using a reference, or only a small reference, you can add the flag -Xmx1g. The only factor determining how much memory BBDuk needs is the number of reference kmers stored, which is linearly proportional to the size of the reference. Only processing large references, or using a high value of РІР‚СљhdistРІР‚Сњ or РІР‚СљedistРІР‚Сњ, actually need a lot of memory. Most operations such as adapter-trimming and quality-trimming need only a tiny amount of memory. You can override this with with the -Xmx flag, e.g. Memory:Р”В«BDukРІР‚в„ўs shellscript will try to autodetect the available memory and use about half of it. BBDuk2 can operate in all 4 modes at once. РІР‚Сљkmask=NРІР‚Сњ 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 РІР‚Сљktrim=rРІР‚Сњ or РІР‚Сљktrim=lРІР‚Сњ must be used. The default is filtering РІР‚вЂњ 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 РІР‚вЂњ 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:Р”В«bduk.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 РІР‚СљinterleavedРІР‚Сњ 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.Р”В«BDukРІР‚в„ўs 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. РІР‚СљDukРІР‚Сњ stands for Decontamination Using Kmers.

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