yueyujiang / GG2_scripts

GG2_scripts

data

• data/rt: 200k tree
• data/aligned_all.filtered.fa.zip: backbone alignment

Select a single copy

To speed up the process, split the sequence file into two files in realtively same size and each ideally contain the same number of genomes.

1. to calculate placement error in edges run
   bash select_copy/select_copy_split.sh tree_file seq_file output_error_file

2. to calculate placement error in path length run
   bash select_copy/dist_err_split.sh tree_file seq_file outdir

uDance

Run
bash udance/run.sh -b backbone_tree_file -s sequence_file -l 10000000 -o outdir -t cores -c 15000

DEPP

Installation

conda env create -f depp_env.yml

Prepare

Run bash scripts/prepare_depp.sh tree_file seq_file outdir

This will

1. Trim the backbone tree and remove sequences in the backbone sequences so that backbone tree and backbone sequences have the same set of species.
2. Make the aligned backbone sequence file to be in four types (full-length, V4, V4 100bp and V4 150bp) by trimming the sequences. Following is the position (index start from 0) we used in the previous run for trimming the squences. Those positions are found by aligning the fragments of 16S to the aligned full-length 16S. It would be good to double check that.

• V4 100 start: 571 End: 669

• V4 150 Start: 571 End: 719

• V4 Start: 571 End: 819

The output will be stored in outdir

• backbone_tree: outdir/backbone.nwk
• backbone_seq: outdir/full_length/backbone.fa, outdir/v4_100/backbone.fa, outdir/v4_150/backbone.fa, outdir/v4/backbone.fa

Training

For each of the backbone sequence type, train a model using the command:
train_cluster_depp.sh -t backbone_tree -s backbone_seq -g gpu_id -o outdir

Placement

Do the placement using the following command:
depp-place-rRNA.sh -q query_seq -a accessory_file -o ourdir -x cores -t mixed.
Pretrain accessory_file can be accessed here

Example

depp-place-rRNA.sh -q data/test_depp/query0.fa -a accessory_file -o ourdir -x cores -t mixed

Others

APPLES (placement)

Installation

pip install apples

Run

run_apples.py -s backbone_seq_file -q query_seq_file -t backbone_tree -o outfile

Treecluster (cluster a tree)

Installation

pip install treecluster

Run

TreeCluster.py -h

UPP (alignment)

Installation

Follow this readme

Run (command I use)

run_upp.py -s seq_to_be_aligned -a backbone_seq -t backbone_tree -A 200 -d otudir -x 36 -p tmp_dir
Note: backbone_tree can be obtained using FastTree: FastTree -nt backbone_seq > backbone_tree