Meryl is the k-mer counter. It is built into the Celera assembler and is also available as a stand-alone application. Meryl uses a sorting-based approach that sorts the k-mers in lexicographical order.

- Jason R. Miller, Arthur L. Delcher, Sergey Koren, Eli Venter, Brian P. Walenz, Anushka Brownley, Justin Johnson, Kelvin Li, Clark Mobarry, Granger Sutton.
*Aggressive assembly of pyrosequencing reads with mates,*

Bioinformatics 2008, vol. 24 (pg. 2818-2824).

Documentation

Important Notes

- Module Name:
`Meryl`(see the modules page for more information) - Implemented as a Singularity container
- Unusual environment variables set
**MERYL_HOME**installation directory**MERYL_HOME**executable directory

Interactive job

Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$End the interactive session:sinteractive --mem=4g[user@cn3316 ~]$module load meryl[+] Loading Meryl 0.0 ... [user@cn3316 ~]$meryl -hmeryl -h usage: meryl ... A meryl command line is formed as a series of commands and files, possibly grouped using square brackets. Each command operates on the file(s) that are listed after it. COMMANDS: print display kmers on the screen as 'kmercount'. accepts exactly one input. count Count the occurrences of canonical kmers in the input. must have 'output' specified. count-forward Count the occurrences of forward kmers in the input. must have 'output' specified. count-reverse Count the occurrences of reverse kmers in the input. must have 'output' specified. k= create mers of size K bases (mandatory). n= expect N mers in the input (optional; for precise memory sizing). memory=M use no more than (about) M GB memory. threads=T use no more than T threads. less-than N return kmers that occur fewer than N times in the input. accepts exactly one input. greater-than N return kmers that occur more than N times in the input. accepts exactly one input. equal-to N return kmers that occur exactly N times in the input. accepts exactly one input. not-equal-to N return kmers that do not occur exactly N times in the input. accepts exactly one input. increase X add X to the count of each kmer. decrease X subtract X from the count of each kmer. multiply X multiply the count of each kmer by X. divide X divide the count of each kmer by X. modulo X set the count of each kmer to the remainder of the count divided by X. union return kmers that occur in any input, set the count to the number of inputs with this kmer. union-min return kmers that occur in any input, set the count to the minimum count union-max return kmers that occur in any input, set the count to the maximum count union-sum return kmers that occur in any input, set the count to the sum of the counts intersect return kmers that occur in all inputs, set the count to the count in the first input. intersect-min return kmers that occur in all inputs, set the count to the minimum count. intersect-max return kmers that occur in all inputs, set the count to the maximum count. intersect-sum return kmers that occur in all inputs, set the count to the sum of the counts. difference return kmers that occur in the first input, but none of the other inputs symmetric-difference return kmers that occur in exactly one input MODIFIERS: output O write kmers generated by the present command to an output meryl database O mandatory for count operations. EXAMPLES: Example: Report 22-mers present in at least one of input1.fasta and input2.fasta. Kmers from each input are saved in meryl databases 'input1' and 'input2', but the kmers in the union are only reported to the screen. meryl print \ union \ [count k=22 input1.fasta output input1] \ [count k=22 input2.fasta output input2] Example: Find the highest count of each kmer present in both files, save the kmers to database 'maxCount'. meryl intersect-max input1 input2 output maxCount Example: Find unique kmers common to both files. Brackets are necessary on the first 'equal-to' command to prevent the second 'equal-to' from being used as an input to the first 'equal-to'. meryl intersect [equal-to 1 input1] equal-to 1 input2

[user@cn3316 ~]$exitsalloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$