Official BBTools Suite by Brian Bushnell

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quality， and contaminant removal. The Swiss Army knife of read processing. bbduk.sh in=reads.fq out=clean.fq ref=adapters.fa ktrim=r k=23 mink=11 hdist=1 tpe tbo BBMerge Paired read merging using neural networks for very low false positive rates. bbmerge.sh in1=r1.fq in2=r2.fq out=merged.fq outu=unmerged.fq Tadpole Fast error correction and assembly for small genomes， taxonomy， amplicons， or other keys. Handles any file size. sortbyname.sh in=reads.fq out=sorted.fq ， viruses。

position， Fast short read aligner optimized for variant calling from Illumina data. Handles reads up to 6kbp. bbmap.sh ref=genome.fa in=reads.fq out=mapped.sam BBDuk Adapter trimming， optimized for metagenomic bins. quickclade.sh bins out=taxonomy.tsv NovaDemux Statistical demultiplexing with error correction for optimal yield and minimal crosstalk. novademux.sh in=reads.fq out=out_%.fq expected=barcodes.txt CallVariants Variant calling from SAM/BAM files with multisample VCF support. callvariants.sh in=mapped.sam ref=genome.fa vcf=vars.vcf CallGenes Gene prediction for prokaryotes， and mitochondria. Also finds 16S/18S/23S/5S/tRNAs. callgenes.sh in=contigs.fa out=genes.gff outa=aminos.faa SortByName Sort reads by name， and metagenomes. tadpole.sh in=reads.fq out=corrected.fq mode=correct Clumpify Reorders reads to reduce file size by 30% on average. Also finds and removes duplicates without alignment. clumpify.sh in=reads.fq out=clumped.fq.gz BBNorm Kmer-based normalization to reduce coverage variation for better assemblies. bbnorm.sh in=reads.fq out=normalized.fq target=100 BBCMS Error correction and low-depth removal for metagenomes with no memory constraints. bbcms.sh in=reads.fq out=corrected.fq SendSketch/BBSketch Rapid taxonomic identification by comparing MinHash sketches to remote databases. sendsketch.sh in=unknown.fa Seal High-speed alignment-free sequence quantification for RNA-seq using kmer matching. seal.sh in=reads.fq ref=transcripts.fa rpkm=rpkm.txt QuickBin Bins metagenomic contigs using coverage and kmer frequencies for metagenome analysis. quickbin.sh in=contigs.fa out=bins *.sam QuickClade Fast taxonomic assignment using kmer frequency spectra， quality filtering。