tree_qa

Assess phylogenetic markers found in each bin.

This optional step of the lineage-specific workflow reports the placement of each bin in the reference genome tree. It must be run on the output folder of the tree command. The -o, --out_format option specifies the desired output:

1. brief summary of genome tree placement indicating the number of unique phylogenetically informative markers found, the number of markers found multiple times, and a taxon string indicating the placement of each bin within the genome tree

2. detailed summary of genome tree placement giving a more detailed indication of where each bin is within the genome tree, general characteristics about each bin (e.g., GC, genome size, coding density), and general characteristics about all reference genomes descendant from the parental node of each bin (e.g., mean and standard deviation of GC)

3. genome tree in Newick format decorated with IMG genome IDs which can be used to examine the phylogenetic neighbours of each bin

4. genome tree in Newick format decorated with taxonomy strings which can be used to examine the phylogenetic neighbours of each bin

5. multiple sequence alignment of reference genomes and bins which can be used to infer a de novo genome tree

Use -f to write results to a file instead of the console, and --tab_table to write tabular outputs as a tab-separated values table instead of a table formatted for console output.

Arguments

usage: checkm tree_qa [-h] [-o {1,2,3,4,5}] [-f FILE] [--tab_table] [-q] [--tmpdir TMPDIR]
                      tree_dir

Assess phylogenetic markers found in each bin.

positional arguments:
  tree_dir              directory specified during tree command

options:
  -h, --help            show this help message and exit
  -o, --out_format {1,2,3,4,5}
                        desired output: (default: 1)
                          1. brief summary of genome tree placement
                          2. detailed summary of genome tree placement including lineage-specific statistics
                          3. genome tree in Newick format decorated with IMG genome ids
                          4. genome tree in Newick format decorated with taxonomy strings
                          5. multiple sequence alignment of reference genomes and bins
  -f, --file FILE       print results to file (default: stdout)
  --tab_table           print tab-separated values table
  -q, --quiet           suppress console output
  --tmpdir TMPDIR       specify an alternative directory for temporary files

Example: checkm tree_qa ./output

Example

checkm tree_qa ./output
checkm tree_qa -o 2 --tab_table -f tree_qa.tsv ./output