Difference between revisions of "CheckM"
Jump to navigation
Jump to search
Moskalenko (talk | contribs) m (Text replacement - "#uppercase" to "uc") |
|||
| (One intermediate revision by the same user not shown) | |||
| Line 1: | Line 1: | ||
| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:Genomics]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|checkm}} | |{{#vardefine:app|checkm}} | ||
| Line 21: | Line 21: | ||
<!--Modules--> | <!--Modules--> | ||
| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
| − | |||
| − | < | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
==System Variables== | ==System Variables== | ||
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
Latest revision as of 18:27, 12 August 2022
Description
CheckM works on a directory of genome bins in FASTA format. By default, CheckM assumes genomes consist of contigs/scaffolds in nucleotide space and that the files to process end with the extension fna. You can specify a different extension with the –x flag. CheckM calls genes internally using prodigal, taking care to identify genes with recoded stop codons. You can call genes externally and provide CheckM with FASTA files containing genes in amino acid space. To specify this, use the --genes flag. Again, you may need to change the extension CheckM looks for (e.g., -x faa).
Environment Modules
Run module spider checkm to find out what environment modules are available for this application.
System Variables
- HPC_CHECKM_DIR - installation directory