samples-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-search-primers

Description

A TAB-delimited file to describe samples and paired-end FASTQ files associated with them. By doing so, this file type links sample names to raw sequencing reads.

This file type includes required and optional columns.

While these required and optional columns are what anvi’o is going to look for anytime you expect to process a TAB-delimited file as samples-txt, you can have as many columns as you like in a given TAB-delimited to be used as samples-txt as long as it includes these required and optional columns.

The following three columns are required for this file type:

• sample: a single-word sample name,
• r1: path to the FASTQ file for pair one, and
• r2: path to the FASTQ file for pair two.

You can also use name as your first column instead of sample.

While you can use relative paths for r1 and r2, it is always better to have absolute paths to improve reproducibility.

The following is an optional column:

• group: A single-word categorical variable that assigns two or more samples into two or more groups. This is useful to co-assemble multiple samples so that you can bin them later.

For more information, see the anvi’o workflow tutorial

Examples samples.txt file

Here is an example file:

sample	group	r1	r2
Sample_01	WARM	/path/to/XXX-01-R1.fastq.gz	/path/to/XXX-01-R2.fastq.gz
Sample_02	COLD	/path/to/YYY-02-R1.fastq.gz	/path/to/YYY-02-R2.fastq.gz
Sample_03	COLD	/path/to/ZZZ-03-R1.fastq.gz	/path/to/ZZZ-03-R2.fastq.gz

Edit this file to update this information.