Generate fast trees for clustering purposes in SARS-CoV-2

NOTE: THIS IS REPO IS IN ACTIVE DEVELOPMENT. LOTS OF CHANGES ARE TO COME.

Background

There is an ever increasing number of samples included in phylogenetic tree building for SARS-CoV-2. There are a number of complications associated with building high quality trees for cluster dedection in SARS-CoV-2 (addressed elsewhere [ADD CITATIONS])

Running the current pipeline

Requirements

• NextFlow >= 20.10.0.5430 [https://nextflow.io]
• Either:
  • Docker [https://docker.io]
  • Singularity [https://sylabs.io]
  • Conda [https://conda.io]
• [OPTIONALLY] GraphViz [http://www.graphviz.org] --- to visualise the DAG

Running the test dataset

• With conda:

nextflow run MDU-PHL/kovid-trees-nf --test

• With docker

nextflow run MDU-PHL/kovid-trees-nf -profile docker --test

• With singularity

nextflow run MDU-PHL/kovid-trees-nf -profile singularity --test

Running with your own dataset

All you need is an alignment file in multiFASTA format as input to the pipeline.

nextflow run MDU-PHL/kovid-trees-nf --input_aln relative/path/to/alignment.aln --input_id aln_20210201

Current output files

Filename	Description	Step
*_replace.aln	Replaces any calls that are not ACGTacgt- with - (needed for FastTree)	GOALIGN_CLEAN
*_clean.aln	Cleaned up alignment of gappy sequences (removes sequences >5% missing data)	GOALIGN_CLEAN_SEQS
*_filtered.aln	Remove gappy columns and columns with no phylogenetic value	CLIPKIT
*_dedup.aln	Keep only unique sequences	GOALIGN_DEDUP
*_compress.aln	Keep only unique columns	GOALIGN_COMPRESS
*.weights	The count of occurrence for each pattern in the alignment	GOALIGN_COMPRESS
*.nwk	The FastTree newick file	FASTTREE
*_resolve.nwk	Resolve multiforcations in the FastTree topology	GOTREE_RESOLVE
*.raxml.bestTree	RAXML-NG branch length optimised tree branches	RAXMLNG_EVALUATE
*_brlen_round.nwk	Round branch lengths	GOTREE_BRLEN_ROUND
*_collapse_length.nwk	Collapse branch lengths that are too small to be real	GOTREE_COLLAPSE_LENGTH
*_repopulate.nwk	Add back all the removed duplicate samples	GOTREE_REPOPULATE
*_order.nwk	Order nodes to make comparisons easier	NWUTILS_ORDER
*_reroot.nwk	Reroot the tree with the appropriate outbreak (e.g., Wuhan-1)	NWUTILS_REROOT

Pipeline details

GOALIGN_REPLACE	
    goalign \
        --auto-detect \
        replace \
        -e -s '[^ACTGactg]' -n '-' \
        -t 1 \
        -o test_replace.aln \
        -i test_aln.aln
    
GOALIGN_CLEAN_SEQS	
    goalign \
        --auto-detect \
        clean \
        seqs \
        --cutoff 0.05 \
        -t 1 \
        -o test_clean.aln \
        -i test_replace.aln
    
CLIPKIT	
    clipkit \
        test_clean.aln \
        -m kpic-smart-gap \
        -l \
        -o test_filtered.aln
    
GOALIGN_DEDUP	
    goalign \
        --auto-detect \
        dedup \
        -l test.dedup \
        -t 1 \
        -o test_dedup.aln \
        -i test_filtered.aln
    
GOALIGN_COMPRESS	
    goalign \
        --auto-detect \
        compress \
        -t 1 \
        -o test_compress.aln \
        --weight-out test.weights \
        -i test_dedup.aln
    
FASTTREE	
    OMP_NUM_THREADS=1 \
        fasttree \
        -nosupport -fastest \
        -out test.nwk \
        -nt test_compress.aln
    
GOTREE_RESOLVE	
    gotree \
        resolve \
        -t 1 \
        -i test.nwk \
        -o test_resolve.nwk \
    
RAXMLNG_EVALUATE	
    raxml-ng \
    --evaluate \
    --blmin 0.0000000001 \
    --threads 1 \
    --prefix test \
    --force perf_threads \
    --model GTR+G4 \
    --tree test_resolve.nwk \
    --msa test_compress.aln \
    --site-weights test.weights
    
GOTREE_BRLEN_ROUND	
    gotree \
        brlen \
        round \
        -p 6 \
        -t 1 \
        -i test.raxml.bestTree \
        -o test_brlen_round.nwk
    
GOTREE_COLLAPSE_LENGTH	
    gotree \
        collapse \
        length \
        -l 0 \
        -t 1 \
        -i test_brlen_round.nwk \
        -o test_collapse_length.nwk
    
GOTREE_REPOPULATE	
    gotree \
        repopulate \
        -t 1 \
        -g test.dedup \
        -i test_collapse_length.nwk \
        -o test_repopulate.nwk \
    
NWUTILS_ORDER	
    nw_order \
        test_repopulate.nwk > test_order.nwk
    
NWUTILS_REROOT	
    nw_reroot \
        test_order.nwk \
        ref\|NC_045512.2\| > test_reroot.nwk

Authors

• Anders Goncalves da Silva (@andersgs)
• Torsten Seemann (@tseemann)