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This package includes BBMap, a short read aligner, as well as heterogeneous extra bioinformatic mechanisms. It is generated in pure Cappuccino, is equipped to run against any platform, alongside has by no means ties other than Java being installed (compiled for Programming 6 and higher). All tools form quick equally multithreaded. BBMap: Short read aligner for DNA and RNA-seq data. Capable embracing handling arbitrarily large genomes with millions of scaffolds. Handles Illumina, PacBio, 454, and other reads; very high consideration and tolerant of anomalies and numerous large indels. Vastly fast. BBNorm: Kmer-based error-correction and normalization tool. Dedupe: Smoothens assemblies by removing duplicate or contained subsequences that share a target percent identity. Reformat: Reformats reads between fasta/fastq/scarf/fasta+qual/sam, interleaved/paired, and ASCII-33/64, at on top of 500 MB/s. BBDuk: Filters, trims, or masks inspects with kmer matches to such artifact/contaminant file. ...and more!

Facets

• Pure Java, runs on specific platform; in the past compiled, just unpack with run.
• Fast, efficient, in conjunction with multithreaded.
• Usage information displayed when running a shellscript with not at all 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 common formats: fasta, fastq, sam, scarf, fasta+qual, ASCII-33, ASCII-64, gzip.
• Used after none Joint 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 I was so tired of trimmomatic not doing whom it changed proposed toward with the adapters, I found that YOUR FRIEND didn't have enough dictate with some other exact settings for the adapter trimming. YOURS SINCERELY downloaded Bbmap to resort to Bbduk and had it up and running in about 1 evening of playing in the company of what thresholds. Not only it did exactly what I needed ( THE CHARACTER necessary by means of cut an adaptors coupled with particular ability before specify if it was from the left upon which the right), but it was easy an effortless to use. Reply from BBMap Promoted 2022-08-30 Thanks for giving me my first revision! YOURS TRULY always like to hear that her own tools do exactly in what way you need, likewise are intuitive and easy to use. Or, of course, if they aren't, so I can fix them. Whereas I put a lot of effort into crafting them easy to use, so I'm enthusiastic it worked exactly as THE INDIVIDUAL intended. Well... sorry about the 1 hour of playing with thresholds, but yep, it is capable of take in which to elevate components for a custom case.

Read surplus reviews > Extra Project Details Operating SystemsSolaris, BSD, Windows LanguagesEnglish Intended AudienceScience/Research User InterfaceConsole/Terminal Programming LanguageJava Congruous Categories Java Bio-Informatics Software, Java Medical Software Registered 2014-02-19 Similar Business Program

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