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============
augur index
============
.. contents:: Table of Contents
:local:
----
.. argparse::
:module: augur
:func: make_parser
:prog: augur
:path: index
Speed up filtering with a sequence index
========================================
As we describe in :doc:`the phylogenetic workflow tutorial <docs.nextstrain.org:tutorials/creating-a-phylogenetic-workflow>`, augur index precalculates the composition of the sequences (e.g., numbers of nucleotides, gaps, invalid characters, and total sequence length) prior to filtering.
The resulting sequence index speeds up subsequent filter steps especially in more complex workflows.
.. code-block:: bash
mkdir -p results/
augur index \
--sequences data/sequences.fasta \
--output results/sequence_index.tsv
The first lines in the sequence index look like this.
.. code-block:: bash
strain length A C G T N other_IUPAC - ? invalid_nucleotides
PAN/CDC_259359_V1_V3/2015 10771 2952 2379 3142 2298 0 0 0 0 0
COL/FLR_00024/2015 10659 2921 2344 3113 2281 0 0 0 0 0
PRVABC59 10675 2923 2351 3115 2286 0 0 0 0 0
COL/FLR_00008/2015 10659 2924 2344 3110 2281 0 0 0 0 0
We then provide the sequence index as an input to augur filter commands to speed up filtering on sequence-specific attributes.
.. code-block:: bash
augur filter \
--sequences data/sequences.fasta \
--sequence-index results/sequence_index.tsv \
--metadata data/metadata.tsv \
--exclude config/dropped_strains.txt \
--output results/filtered.fasta \
--group-by country year month \
--sequences-per-group 20 \
--min-date 2012
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