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Is it possible to include BBMap in Bcbio-nextgen pipeline?

Is it possible to include BBMap in Bcbio-nextgen pipeline? Are there any examples and tutorials on that software besides those posted on their website? Thanks.

seq wg soft sequencing
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updated by Brad Chapman Brad Chapman • written by elvissober • elvissober

I'm currently in the process of writing guides for most of the tools in the BBMap package... I've finished several, and BBMap is on my list for this week.

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updated by Ram Ram • written by Brian Bushnell Brian Bushnell

1 answer

It's possible to include it, but it would need integration work to include it as a new aligner. Documentation on writing that code is here:

https://bcbio-nextgen.readthedocs.org/en/latest/contents/code.html#aligner

Out of curiousity, why do you prefer BBMap over other integrated aligners in bcbio like bwa mem?

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written by Brad Chapman Brad Chapman

I'm curious about BBMap as well. Brian seem to be quite a comprehensive resource on Biostars, so maybe he can comment. Things I can glean from the internet:

- BBMap uses a semi global alignment algorithm instead of local Smith-Waterman

- There's this poster where Brian benchmarks on synthetic data with varying mismatches and indel sizes, showing good performance for large gaps in alignment/reference coordinates.

- The SAM output is TopHat compatible - so maybe this is designed for RNAseq applications?

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written by Matt Shirley Matt Shirley

So, yes, BBMap is designed for RNA-seq and DNA-seq, and it outperforms all other aligners I've tested when dealing with long indels (or indels in general, but particularly long ones), accuracy-wise. It's also good at aligning very-highly-mutated sequences or very low-quality data. BWA-mem has an advantage in memory use and (usually) alignment speed, though. And while this aspect is not very important with human resequencing, BBMap has a huge advantage in index-building time over other aligners; this is actually quite important when analyzing large numbers of de-novo assemblies of different organisms with different assemblers and parameters.

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updated by Ram Ram • written by Brian Bushnell Brian Bushnell

I just have tried it and it does the job of producing .sam. However could not find a better software than Nextgen. Does anybody has a clear tutorial on using that ncbio for wgs from .sra to vcf? Thx.

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updated by Ram Ram • written by elvissober • elvissober

Need a clear tutorial on how to add tuberculosis microbe to that software and how to run a pipeline to process from a set of .sra files to .vcf and .pdf reports, thx

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written by elvissober • elvissober

For processing with sra you'll want to convert into standard fastq format using the SRA toolkit (http://www.ncbi.nlm.nih.gov/books/NBK158900/). In bcbio, you can add a custom reference genome for tuberculosis (https://bcbio-nextgen.readthedocs.org/en/latest/contents/configuration.html#adding-custom-genomes) and then run a standard variant calling pipeline by creating a configuration file (https://bcbio-nextgen.readthedocs.org/en/latest/contents/configuration.html#automated-sample-configuration). I haven't personally called on tuberculosis so don't have any species specific tips but hope this helps for getting started.

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written by Brad Chapman Brad Chapman

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