From 3eababafe1c0e05af7b2e8a50bb67c46822852e2 Mon Sep 17 00:00:00 2001 From: Arjun Prasad Date: Tue, 6 Aug 2024 15:54:58 -0400 Subject: [PATCH] Updates to various sections for v1.0.24 --- README.md | 38 +++++++++++++++++++++++++++++--------- 1 file changed, 29 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index 83286bd..8657223 100644 --- a/README.md +++ b/README.md @@ -55,11 +55,23 @@ If you install BLAST via conda in this way you will need to run `conda activate - `--output ` or `-o ` Write the output to \ instead of STDOUT +- `--nucleotide_output ` Output the nucleotide sequence for any identified stx operons (includes partial and full length operons) + - `--blast_bin ` Directory to search for tblastn binary. Overrides environment variable `$BLAST_BIN` and the default PATH. - `-q` or `--quiet` Suppress the status messages normally written to STDERR. -- `--log ` Error log file, appended and opened when you first run the application. This is used for debugging +- `--log ` Error log file, appended and opened when you first run the application. This is used for debugging. + +- `--debug` Run in debug mode. Additional messages are printed and files in $TMPDIR are not removed after running. + +### For AMRFinderPlus + +These options are not expected to be used outside of the [AMRFinderPlus](https://github.com/ncbi/amr/wiki) pipeline. + +- `--amrfinder` Output in [AMRFinderPlus](https://github.com/ncbi/amr/wiki) format + +- `--print_node` Add column for [Hierarchy node](https://www.ncbi.nlm.nih.gov/pathogens/docs/gene_hierarchy/) optionally reported by AMRFinderPlus. ## Output @@ -67,11 +79,10 @@ The output of StxTyper is a tab-delimited file with the following fields, all pe 1. __target_contig__: The contig identifier from the input FASTA file 2. __stx_type__: The stx type called by the algorithm, for "operon = COMPLETE" - it will be stx plus two characters (e.g., stx1a), for other values of operon stx_type will be - stx1, stx2, or just stx if it can't resolve at all. + it will be stx plus two characters (e.g., stx1a), for other values of operon + stx_type will be stx1, stx2, or just stx if it can't resolve at all. 3. __operon__: What status the operon was found to be. It can be - - __COMPLETE__ for complete and fully typeable - known stx types + - __COMPLETE__ for complete and fully typeable known stx types - __PARTIAL__ for partial operons that are internal to contigs and not terminating at contig boundaries - __PARTIAL_CONTIG_END__ for partial operons that could be split by contig @@ -82,6 +93,9 @@ The output of StxTyper is a tab-delimited file with the following fields, all pe nonsense mutation - __FRAMESHIFT__ where StxTyper detected an indel in the coding sequence that would cause a frame shift in one or more of the subunits + - __AMBIGUOUTS__ StxTyper found an ambiguous base in the query sequence + (e.g., N), this could be the result sequencing or assembly error so the + user might want to take a closer look at the sequence. - __COMPLETE_NOVEL__ a full-length stx operon that is not typeable using the current scheme 4. __identity__ The combined percent identity for both A and B subunits @@ -92,12 +106,18 @@ The output of StxTyper is a tab-delimited file with the following fields, all pe none aligned 9. __A_identity__ The percent identity to the reference for the A subunit, empty if none aligned -10. __A_coverage__ The percentage of the reference for the A subunit that is +10. __A_reference_subtype__ The subtype assigned to the reference sequence for +the A subunit. Note this may be different from the subtype for the operon as a +whole. +11. __A_coverage__ The percentage of the reference for the A subunit that is covered by the alignment, empty if none aligned -11. __B_reference__ The closest reference protein for the B subunit, empty if +12. __B_reference__ The closest reference protein for the B subunit, empty if none aligned -12. __B_identity__ The percent identity to the reference for the B subunit, +13. __B_reference_subtype__ The subtype assigned to the reference sequence for +the B subunit. Note this may be different from the subtype for the operon as a +whole. +14. __B_identity__ The percent identity to the reference for the B subunit, empty if none aligned -13. __B_coverage__ The percentage of the reference for the B subunit that is +15. __B_coverage__ The percentage of the reference for the B subunit that is covered by the alignment, empty if none aligned