bin

BIN

A BIN-type anvi’o artifact. This artifact is typically generated, used, and/or exported by anvi’o (and not provided by the user)..

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Provided by

anvi-cluster-contigs anvi-display-pan anvi-interactive anvi-refine anvi-rename-bins anvi-script-add-default-collection anvi-script-compute-bayesian-pan-core

Required or used by

anvi-display-metabolism anvi-estimate-metabolism anvi-estimate-scg-taxonomy anvi-estimate-trna-taxonomy anvi-gen-fixation-index-matrix anvi-gen-gene-level-stats-databases anvi-gen-variability-profile anvi-get-short-reads-from-bam anvi-get-split-coverages anvi-inspect anvi-interactive anvi-merge-bins anvi-refine anvi-rename-bins anvi-script-gen-distribution-of-genes-in-a-bin

Description

In its simplest form, a group of items that are put together. Think of a literal bin in which you put data. One or more bins in anvi’o form a collection.

In anvi’o, a bin may reprsent one or more contigs, or gene clusters, or any item that can be shown in the interactive interface and stored in a profile-db, pan-db, or genes-db.

Bin names become handy to specifically target a group of items to investigate via programs such as anvi-refine or anvi-split, specify a group of contigs in files such as internal-genomes, or find them in output files anvi’o generates via programs such as anvi-summarize or anvi-estimate-genome-completeness.

Since they are a part of the umbrella concept collection, information about bins are stored in various anvi’o databases, each of which can be used with the program anvi-show-collections-and-bins to see the bin content.

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