Microbial 'omics


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collection-txt [artifact]

Table of Contents

TXT

A TXT-type anvi’o artifact. This artifact can be generated, used, and/or exported by anvi’o. It can also be provided by the user for anvi’o to import into its databases, process, and/or use.

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Provided by

anvi-export-collection

Required or used by

anvi-import-collection anvi-script-get-coverage-from-bam anvi-script-merge-collections

Description

This is a two-column TAB-delimited file without a header that describes a collection by associating items with bin names. It can be used to import or export collections in and out of anvi’o databases, and/or transferring them between anvi’o projects.

The first column in the file lists item names and the second column associates a given item with a bin.

item_01 bin_1 item_02 bin_1 item_03 bin_1 item_04 bin_2 item_05 bin_3 item_06 bin_3

The optinal bins info file

In addition to the essential file above, you can associate an optional TAB-delmited file with three columns with a collection to provide information about ‘bins’ in it, such as their source, and/or color to be used when they are displayed in summary outputs or anvi’o interactive interfaces. Here is an example:

bin_1	N/A	 #c9d433
bin_2	N/A	 #e86548
bin_3	N/A	 #0b8500

In this file format the first column is a bin name, the second column is a source, and the third column is an HTML color.

The source is a free form text and can be anything. We often use anvi-interactive or CONCOCT or anvi-refine for our bins to track which ones were manually refined, and which ones were coming from an automated binning algorithm.

You can provide this optional file to the program anvi-import-collection with the parameter --bins-info.

Edit this file to update this information.