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This package includes BBMap, a short interpret aligner, as optimally on the grounds that various opposite bioinformatic tools. It is scribbled beneath pure Java, can run on any system, and has no dependencies diverse than Java being installed (compiled toward Java 6 along with higher). All assets are functioning and multithreaded. BBMap: Short read aligner for DNA and RNA-seq statistics. Capable of handling arbitrarily large genomes in the presence of millions of scaffolds. Handles Illumina, PacBio, 454, not to mention other reads; very high sensitivity and tolerant of errors and numerous huge indels. Extremely fast. BBNorm: Kmer-based error-correction and normalization tool. Dedupe: Reduces complexity assemblies by removing matching version or contained subsequences that share a end rate identity. Restructure: Reformats analyzes between fasta/fastq/scarf/fasta+qual/sam, interleaved/paired, and ASCII-33/64, at over 500 MB/s. BBDuk: Refiners, trims, or masks reads together with kmer matches to an artifact/contaminant file. ...and more!

Features

• Pure Java, runs on any platform; at this stage compiled, just uncompress besides run.
• Fast, efficient, moreover multithreaded.
• Usage information displayed when galloping selected shellscript with definitely not parameters.
• Highest sensitivity of any short-read aligner.
• Easy to install - just unzip/untar.
• Easy to use. Example: bbmap.sh ref=ecoli.fa in=reads.fq out=mapped.sam
• Handles all popular formats: fasta, fastq, sam, scarf, fasta+qual, ASCII-33, ASCII-64, gzip.
• Used by the Union Genome Institute.
• BB stands for Bestus Bioinformaticus.
• There is a handy FAQ here: http://seqanswers.com/forums/showthread.php?t=58221

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• yuli9691 Posted 2022-07-15 THE AUTHOR was so tired as for trimmomatic irrelevant doing why the object grew supposed to with the adapters, I found that ONE didn't obtain enough control in addition to the complete settings for the adapter trimming. I downloaded Bbmap toward use Bbduk and had it up and running in about 1 h of playing with the thresholds. Not only it did literally what I needed ( I needed to incise individual adaptors besides none ability until specify for fear that it was from the left in place of the right), otherwise it transformed easy an intuitive to use. Reply from BBMap Posted 2022-08-30 Thanks for giving me my first review! THIS PERSON invariably like to sense that my tools do exactly what you ask for, and are intuitive and basic to use. Or, embracing course, if they aren't, so I can fix the people. But THE PERSON IN QUESTION put a a large quantity of effort onto the interior of making the group easy to use, so I'm glad it worked exactly as I intended. Well... apologetic about the 1 hour of playing with thresholds, but yep, it can take that to optimize objects for unique custom case.

Read enhanced assessments > Additional Mission Details Operating SystemsSolaris, BSD, Transoms LanguagesEnglish Intended AudienceScience/Research Customer InterfaceConsole/Terminal Programming LanguageJava Related Hierarchies Java Bio-Informatics Software, Java Medical Solution Registered 2014-02-19 Similar Business Software

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