Microbial 'omics


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primers-txt [artifact]

Table of Contents

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-script-get-primer-matches

Description

A TAB-delimited file to describe primer sequences. A primer sequence can be exact (such as ATCG), or fuzzy (such as AT.G, which would match any combination of ATAG, ATTG, ATCG, or ATGG). Fuzzy primers are defined by regular expressions, properties of which are explained best in the Python documentation, or cheatsheets like this one.

This file type includes two required and any number of user-defined optional columns.

The following three columns are required for this file type:

  • name: a single-word name for a given primer,
  • primer_sequence: the primer sequence.

An example primers-txt file

Here is an example file with three primers:

name primer_sequence
PR01 AA.A..G..G..G.CCG.C.A.C
PR02 AACACCGCAGTCCATGAGA
PR03 A[TC]A[CG]T[ATC]TCGAGC

Edit this file to update this information.