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CZ ID Long-Read mNGS workflow

​ The CZ ID mNGS Nanopore pipeline was developed in collaboration with the bioinformatics team from Oxford Nanopore Technologies (ONT). ​ The documentation presented here reflects the current CZ ID long-read-mngs pipeline status and processes, with descriptions of the parameters used. ​ Further documentation on how to use the CZ ID long-read-mngs workflow can be found on the CZ ID help center -- including a pipeline overview outlining the pipeline steps and details of the initial validation. ​

Changelog

v0.7.8 -- May 21, 2024 -- Adjust Diamond sensitivity ​

  • Parameterizes the WDL version for the Diamond workflow. It is now a top-level input to the long-read-mngs WDL workflow.
  • Added the --sensitive flag to Diamond invocations.
  • Fixed an issue where certain network requests failed due to an interaction between Docker and the Python requests module. ​

v0.7.7 -- April 29, 2024 -- Prioritize more specific taxon-level hits ​

  • Changed some of the code that calls hits for read and contig queries to prioritize more specific hits over more general ones, i.e. species-level hits will be prioritized over genus-level, and genus-level over family-level. The most specific hit available will be chosen. ​

v0.7.6 -- March 8, 2024 -- Bugfix for coverage viz output ​

  • Fixed a bug that caused coverage viz output files to output the wrong contig file byteranges for contigs. Previously, the byteranges being output were for an intermediate file (one that filtered out contigs that did not have a corresponding read). GenerateCoverageViz now uses the full contigs file, which is a workflow output, as input and generates contig byteranges for this file. ​

v0.7.5 -- Nov 30, 2023 -- Expand scope of when we generate coverage vizualizations ​

  • Enable coverage vizualizations to be generated for taxa that only have loose NT reads (i.e., taxa with no contigs but that have at least 1 NT read). ​

v0.7.3 -- May 19, 2023 -- Fix bug in reads to contigs step that caused it to fail for long contigs ​

  • Fix bug in reads to contigs step that caused it to fail for long contigs. ​

v0.7.2 -- April 25, 2023 -- Algorithmic updates to improve coverage of taxa identified in samples ​

  • Stitches together multiple hits from the same read or contig to the same accession into longer hits. These hits still show up in their original, separate, form in the coverage visualization. ​

v0.7.0 -- April 25, 2023 -- Algorithmic updates to improve coverage of taxa identified in samples ​

  • Updates the Flye version used from v2.9.0 to v2.9.2
  • Increases the stringency of alignment when mapping reads to their respective contigs (in the RunReadsToContigs step) by requiring that <20% of the read be clipped. This increases the number of "loose reads" but reduces spurious assignment of reads to contigs.
  • Modifies the minimap2 command for NCBI NT alignment (in the RunNTAlignment step) to use map-ont instead of previously-used asm20. This adjustment compliments the new stringency by improving the mapping of reads that don't belong to contigs. ​

v0.6.0 -- April 4, 2023 -- Initial pipeline release