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workflows/index-generation/helpful_for_analysis/README.md

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+### jupyter notebooks used for helpful common analysis steps including:
+* querying NCBI for an accession and lineage (used to investigate reads in the "all taxa with neither family nor genus classification" report for mNGS)
+* querying marisa trie files - notebook to easily query all marisa trie files generated from index generation workflow above.
+* compare non host alignment times between two projects - this was used to benchmark how long it took to do non host alignment on old and new indexes.
+* generate taxon lineage changelog for a sample report - get a readout on which reads from a sample report have a taxon / lineage change between new and old index runs. Used for comp bio validation purposes mainly.
+* checking sequence retention for different index compression runs - this notebook was handy for running multiple compression runs and summarizing which reads were dropped, helpful for early analysis and benchmarking of compression workflow.