Bob Literman
Bob Literman
Certain tools in the SISRS pipeline (namely BAMTools) can fail for one reason or another and don't throw an explicit error when it happens. This makes restarting SISRS after 1...
Hello all, As @anderspitman found earlier, different versions of Bowite2 give slightly different mapping data. I noticed that in the Docker version is using v.2.3.3.1, while I was using 2.3.4...
SISRS can generate a run ID (x random numbers) and a log file. The log file could include things like program versions, mapping stats, final stats, but without the intermediate...
Future thought: Instead of subsampling reads randomly, perhaps we could be assembling better genomes and getting more representative mapping if we instead: 1) Get raw reads for X species 2)...
Hi @anderspitman, After bringing over the new Python port branch, there are a few things that I'm unclear about. Would you mind creating a basic README with usage instructions (how...
Hey @anderspitman, One major bottleneck with SISRS is that the Bowtie mapping steps occur serially, rather than in parallel. In part, this is because Bowtie itself does not run in...
Include an option to identify specific taxa which lead to disproportionate amounts of missing data for possible downstream filtering
Subsampling via BBMap suite can specify total final desired bases, eliminating need to take read length into account.
When running the SISRS program with data from 8 ape species each ~10X coverage, the specific_genome.py script fails due to insufficient memory (Run on BlueWaves cluster on 1 node, 20ppn,...