nextstrain / tb

Nextstrain build for tuberculosis

nextstrain.org/tb

This is the Nextstrain build for tuberculosis, visible at nextstrain.org/tb.

The build encompasses preparing data for analysis, doing quality control, performing analyses, and saving the results in a format suitable for visualization (with auspice). This involves running components of Nextstrain such as augur and auspice.

All tuberculosis-specific steps and functionality for the Nextstrain pipeline should be housed in this repository.

Tutorial

There is a tutorial on how to run this build.

Usage

If you're unfamiliar with Nextstrain builds, you may want to follow our quickstart guide first and then come back here.

The easiest way to run this pathogen build is using the Nextstrain command-line tool:

nextstrain build .

See the nextstrain-cli README for how to install the nextstrain command.

Alternatively, you should be able to run the build using snakemake within an suitably-configured local environment.
Details of setting that up are not yet well-documented, but will be in the future.

Build output goes into the directories results/ and auspice/.

Once you've run the build, you can view the results in auspice:

nextstrain view auspice/

Configuration

Configuration takes place entirely with the Snakefile. This can be read top-to-bottom, each rule specifies its file inputs and output and also its parameters. There is little redirection and each rule should be able to be reasoned with on its own.

tb's Issues

can't establish a connection to the server at localhost:4000.

Dear nexstrain team

I am trying to reproduce the TB tutorial, I wanted to visualize tb.json within the auspice folder. I tried to visualize it by using auspice conda env

Current Behavior
Unable to connect http://localhost:4000

Expected behavior
visualize tb.json by using auspice conda env

Your environment: if running Nextstrain locally

• Operating system: Linux 3.19.0-80-generic x86_64
• Browser: firefox and google chrome
• Version (e.g. auspice 2.7.0): 2.17.1
  
  

many thanks in advance

Johanna

Rename `master` to `main`

Context

Overarching (internal) context

Bug in refine step

@emmahodcroft ---

I was just working through the tb tutorial here at https://nextstrain.org/docs/getting-started/tb-tutorial. With my local version of augur (on master) and with the lastest version of the Docker image from the CLI (augur version 3.0.5.dev1) I'm getting the following error:

nextstrain:/nextstrain/build $ augur refine \
>     --tree results/tree_raw.nwk \
>     --alignment results/masked.vcf.gz \
>     --vcf-reference data/ref.fasta \
>     --metadata data/meta.tsv \
>     --timetree \
>     --root residual \
>     --coalescent opt \
>     --output-tree results/tree.nwk \
>     --output-node-data results/branch_lengths.json

Inferred a time resolved phylogeny using TreeTime:
	Sagulenko et al. TreeTime: Maximum-likelihood phylodynamic analysis
	Virus Evolution, vol 4, https://academic.oup.com/ve/article/4/1/vex042/4794731

Traceback (most recent call last):
  File "/usr/bin/augur", line 11, in <module>
    load_entry_point('nextstrain-augur', 'console_scripts', 'augur')()
  File "/nextstrain/augur/augur/__main__.py", line 10, in main
    return augur.run( argv[1:] )
  File "/nextstrain/augur/augur/__init__.py", line 61, in run
    return args.__command__.run(args)
  File "/nextstrain/augur/augur/refine.py", line 189, in run
    node_data['clock'] = {'rate': tt.date2dist.clock_rate,
AttributeError: 'NoneType' object has no attribute 'clock_rate'

Are you able to reproduce this?

BTW I've made a Travis build here: https://travis-ci.com/nextstrain/tb that reproduces this behavior.

small bug in tutorial

Hi,
I found a small bug in the tutorial on https://nextstrain.org/docs/tutorials/tb, because it throws an error with the output definition.

I think, instead of:

augur ancestral \
    --tree results/tree.nwk \
    --alignment results/masked.vcf.gz \
    --vcf-reference data/ref.fasta \
    --inference joint \
    --output results/nt_muts.json \
    --output-vcf results/nt_muts.vcf

it should say:

augur ancestral \
    --tree results/tree.nwk \
    --alignment results/masked.vcf.gz \
    --vcf-reference data/ref.fasta \
    --inference joint \
    --output-node-data results/nt_muts.json \
    --output-vcf results/nt_muts.vcf