bams-and-profiles-txt

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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Provided by

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.

Required or used by

anvi-report-inversions

Description

A TAB-delimited file to describe anvi’o single-profile-db and bam-file pairs along with the contigs-db used the profile the BAM file.

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.

Example

Here is an example file:

name	contigs_db_path	profile_db_path	bam_file_path
D01	CONTIGS.db	D01/PROFILE.db	D01.bam
R01	CONTIGS.db	R01/PROFILE.db	R01.bam
R02	CONTIGS.db	R02/PROFILE.db	R02.bam

Optional columns

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: r1 and 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:

name	contigs_db_path	profile_db_path	bam_file_path	r1	r2
D01	CONTIGS.db	D01/PROFILE.db	D01.bam	D01-R1.fastq	D01-R2.fastq
R01	CONTIGS.db	R01/PROFILE.db	R01.bam	R01-R1.fastq	R01-R2.fastq
R02	CONTIGS.db	R02/PROFILE.db	R02.bam	R02-R1.fastq	R02-R2.fastq

Some programs, such as anvi-report-inversions, can process the r1 and r2 files.

Edit this file to update this information.