BBMap is multithreaded for both indexing and mapping. After indexing, there are two stages of processing for each read, mapping finding candidate locations via kmer matching and alignment scoring how well the read matches each candidate location. Normally, BBMap spends most of its time in the alignment rather than mapping phase. Speeding up mapping also speeds up alignment, because fewer candidate sites need to be examined.
Generally, any flag that increases speed reduces sensitivity, and vice-versa. Maxindel has more impact on insertions than deletions, because deletions relative to the reference can be found that are much longer than read length, but it is impossible to find an insertion longer than read length from mapping a single read.
The default for maxindel is The same is true if you are looking for severe mutations like knocked-out genes. To increase speed, or to avoid spurious long indels caused by chimeric sequences MDA, for example , you can reduce it to a lower value like There are various optional flags such as idfilter and subfilter that ban alignments failing those filters.
BBMap requires read input to be fasta or fastq, compressed or raw. Paired reads can be in two files or interleaved in a single file. It cannot process both paired and unpaired reads in the same run except by using BBWrap. The indexing phase requires fasta format only compressed is OK. Output formats are fasta, fastq, sam, or bam if samtools is installed. All other output statistics, histograms, coverage, etc are tab-delimited text, with one or more header rows starting with and the rest data.
All reads go to out. Pairs are always kept together; if one read is mapped and the other is unmapped, both will go to outm. BBMap supports paired reads. That simply drops the innie orientation requirement for pairing. For information on the syntax of using paired reads, please see UsageGuide.
BBMap generates coverage information by internally using Pileup. So, the results are the same as generating a sam file with BBMap and feeding it to pileup. However, Pileup supports a wider variety of parameters, so there may be cases where it is preferable. The cigar string is a required field in a Sam file, which tells you how the read aligned to the reference.
That was fixed several years ago in the Sam 1. Unfortunately, some old or unmaintained pieces of software do not correctly support this. BBMap is a global aligner. That means it looks for the highest-scoring alignment taking into account all bases in a sequence.
A local aligner would look for the best-scoring local alignment, meaning an alignment where the ends are possibly clipped off. So, if there were two possible alignment locations for a bp read, one with 3 mismatches scattered through a read, and one with 5 mismatches all in the last 10bp of a read, BBMap would place the read at the location with 3 mismatches, while a local aligner would probably place it at the location with 5 mismatches, but clip the end so that the result would be a clipped 90bp sequence with zero mismatches.
Which of these is better depends on the experiment, but global alignments are essential in order to detect long indels. That does not make it a local aligner — it still looks for the best global alignment. If the local flag is enabled, then the alignment will be clipped if that yields a higher score. So, BBMap will create local alignments, but it will not guarantee that it finds the optimal local alignment — rather, it will produce local alignments from the optimal global alignments.
Internally, BBMap uses a custom affine-transform matrix to generate alignment scores. These numbers were determined empirically through extensive testing. A second consecutive mismatch only gets a point penalty, and the exact penalties continue to change with the length of a mutation event, and type — sub versus insertion versus deletion. However, this is very confusing to users. How is that decided? So, setting either of these higher will increase speed at the expense of sensitivity. This is almost as fast, and also requires all bases to match the reference, but allows read bases to map to reference Ns, or for reads to go off the end of contigs.
Normal BBMap supports reads up to bp. Reads longer than the max read length can be automatically shredded and renamed by adding the flag maxlen, e. The PacBio versions have a different error weight profile designed for long reads with a high error rate, dominated by short indels. It can process Illumina data but the globally optimal alignments will occasionally differ between the two versions. It is also the recommended version for Nanopore data.
Skimmer is designed to find all alignments above a certain threshold, as opposed to the normal versions, which attempt to find the single best alignment, and some alignments that are almost as good like the second and third best , to quantify whether the best alignment is ambiguous.
User Diesel on the Crackberry. I tried it on my BlackBerry Bold running 4. Above is a screenshot of my BlackBerry after the install process. Nice and smooth and it put the icon back. You are commenting using your WordPress. You are commenting using your Google account. You are commenting using your Twitter account. You are commenting using your Facebook account. Notify me of new comments via email. Notify me of new posts via email.
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