CheckM qa (version 1.2.5+galaxy0)

Marker for assessing bins:

Each marker to exclude should be listed on a separate line of the file. Output of the CheckM lineage_set or taxon_set tools

Marker gene HMM info for each bin:

Output of the CheckM analyze tool

Marker gene bin stats:

Output of the CheckM analyze tool

Marker gene HMM hits to each bin:

Output of the CheckM analyze tool

Desired output:

Markers to exclude from marker sets:

Treat marker as independent?:

It will ignore co-located set structure

Do not exclude adjacent marker genes when estimating contamination?:

Skip identification and filtering of pseudogenes?:

AAI threshold used to identify strain heterogeneity:

Ignore model-specific score thresholds?:

E-value cut off:

Percent overlap between target and query:

Coverage of each sequence:

Generated by the coverage command

Extra outputs:

What it does

CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. It provides robust estimates of genome completeness and contamination by using collocated sets of genes that are ubiquitous and single-copy within a phylogenetic lineage. Assessment of genome quality can also be examined using plots depicting key genomic characteristics (e.g., GC, coding density) which highlight sequences outside the expected distributions of a typical genome. CheckM also provides tools for identifying genome bins that are likely candidates for merging based on marker set compatibility, similarity in genomic characteristics, and proximity within a reference genome tree.

This command identifies marker genes in bins and calculates genome statistics

Adjacent called genes matching the same marker gene may indicate a true duplication event, a gene calling error, or an assembly error. If adjacent genes hit distinct regions of the same marker gene HMM, CheckM assumes a gene calling error has occurred and concatenate the two genes. When this occurs, CheckM concatenates the gene ids of the two genes with a pair of ampersands (&&).

Outputs

Output in function of selection output format

Summary of bin completeness, contamination, and strain heterogeneity

Bin Id: bin identifier derived from input FASTA file Marker lineage: indicates lineage used for inferring marker set (a precise indication of where a bin was placed in CheckM's reference tree can be obtained with the tree_qa command) No. genomes: number of reference genomes used to infer marker set No. markers: number of inferred marker genes No. marker sets: number of inferred co-located marker sets 0-5+: number of times each marker gene is identified Completeness: estimated completeness Contamination: estimated contamination Strain heterogeneity: estimated strain heterogeneity
Extended summary of bin quality (includes GC, genome size, coding density, ...)
Summary of bin quality for increasingly basal lineage-specific marker sets

Node Id: unique id of internal node in genome tree from which lineage-specific markers were inferred
ist of marker genes for each bin along with the number of times each marker was identified

Node Id: unique id of internal node in genome tree from which lineage-specific markers were inferred Marker lineage: indicates lineage used for inferring marker set Useful for identifying lineage-specific gene loss or duplication
List of bin id, marker gene id, and called gene id for each identified marker gene
List of marker genes present multiple times in a bin
List of marker genes present multiple times on the same scaffold

Useful for identifying true gene duplication events, gene calling errors, or assembly errors. See note below.
List indicating the position of each marker genes within a bin
Marker genes identified in each bin and their sequence