viral-ngs
viral-ngs copied to clipboard
broadinstitute
Viral genomics analysis pipelines
add `bbmap.BBMapTool().dedup_clumpify()`, along with unit tests; pass `JVMmemory` to bbmap and clumpify; add `rmdup_clumpify_bam` to `read_utils.py`; change `TestRmdupUnaligned `unit tests for bbmap to use `read_utils.py::rmdup_clumpify_bam`; add `dedup_bam` WDL task to...
based on tile count or flowcell suffix
To address https://github.com/broadinstitute/viral-classify/issues/1, this adds a new command, `krakenuniq_report_filter`, to `metagenomics.py`: ``` usage: metagenomics.py subcommand krakenuniq_report_filter [-h] [--fieldToFilterOn {num_reads,uniq_kmers}] [--fieldToAdjust {num_reads,uniq_kmers} [{num_reads,uniq_kmers} ...]] [--keepAboveN KEEP_THRESHOLD] [--loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL,EXCEPTION}] [--version] [--tmp_dir TMP_DIR]...
Hi, do you have any tutorial and jupyter notebook which describe step by step viral metagenomics using viral-ngs it would be great if you share it with me Regards
The old mvicuna post-processing code expects read IDs to have a `/1` mate suffix, and only includes those that do, which single-end reads do not have (nor interleaved fastqs, but...
When determining GATK version (e.g. for choosing version-specific switches), base it on the actual GATK jar, rather than on tools.gatk.TOOL_VERSION_TUPLE . Fix how GATK jar is extracted in refine_2x_and_plot task....
The command line function `fastq_to_bam` exists as part of `read_utils.py`, however it is not currently exposed via WDL. A task to call the function should be added to `tasks_read_utils.wdl` and...
Zstd has a nonstandard python api which requires customization. Also allows for multithreading compression.
