A TXT-type anvi’o artifact. This artifact is typically provided by the user for anvi’o to import into its databases, process, and/or use.
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There are no anvi’o tools that generate this artifact, which means it is most likely provided to the anvi’o ecosystem by the user.
This file type includes required and optional columns. The following four columns are required for this file type:
name: a single-word name for the entry.
contigs_db_path: path to a contigs-db.
bam_file_path: path to a bam-file.
profile_db_path: path to a single-profile-db generated from the BAM file and the contigs database mentioned.
Here is an example file:
In addition to the required columns shown above, you can add as many columns as you like in your file. But two of these columns will be further processed during sanity check:
r2, whith the expectation that these columns will include information regarding the location of the raw FASTQ files. For each row the bams-and-profiles-txt file describes, the FASTQ files must be those that were used to generate the BAM files. Here is an example file with these two additional columns:
Some programs, such as anvi-report-inversions, can process the
Edit this file to update this information.