meryl - in- and out-of-core kmer counting and utilities

Description

meryl computes the kmer content of genomic sequences.  Kmer content is represented as a list of kmers and
       the number of times each occurs in the input sequences.  The kmer can be restricted to only  the  forward
       kmer,  only the reverse kmer, or the canonical kmer (lexicographically smaller of the forward and reverse
       kmer at each location).  Meryl can report the histogram of counts, the list of kmers and their counts, or
       can perform mathematical and set operations on the processed data files.

       The output of meryl is two binary files, called a meryl database, which can be quickly dumped to  provide
       a histogram of counts, or the actual counts.  A C++ library is supplied for direct access to the files.

Example

Batchcreationofatable
       Initialize  the  compute  with  -configbatch, which needs all the build options.  Execute all -countbatch
       jobs, then -mergebatch to complete.

              meryl -configbatch-B [options] -o file
              meryl -countbatch 0 -o file
              meryl -countbatch 1 -o file
              ...
              meryl -countbatch N -o file
              meryl -mergebatch N -o file

Name

       meryl - in- and out-of-core kmer counting and utilities

Options

-P Estimate memory requirements. Given a sequence file (-s) or an upper limit on the number of mers
in the file (-n), compute the table size (-t in build) to minimize the memory usage. This mode
recognizes the following options:

-m# size of a mer (required)

-c# homopolymer compression (optional)

-p enable positions

-sseq.fasta
Sequence file to be scanned to determine the number of mers

-n# compute params assuming file with this many mers in it

Only one of -s, -n need to be specified. If both are given, -s takes priority.

-B Compute the mer-count tables given a sequence file (-s) and lots of parameters. By default, both
strands are processed.

-f only build for the forward strand

-r only build for the reverse strand

-C use canonical mers (assumes both strands)

-L# DON'T save mers that occur less than # times

-U# DON'T save mers that occur more than # times

-m# size of a mer (required)

-c# homopolymer compression (optional)

-p enable positions

-sseq.fasta
sequence to build the table for

-otblprefix
output table prefix

-v entertain the user

The meryl process can run in one large memory batch, in many small memory batches, or under SGE
control, all with or without using multiple CPU cores. By default, the computation is done as one
large sequential process. Multi-threaded operation is possible, at additional memory expense, as
is segmented operation, at additional I/O expense.

Threadedoperation
Split the counting in to n almost-equally sized pieces. This uses an extra h MB (from -P)
per thread.

-threadsn
use n threads to build

Segmented,sequentialoperation
Split the counting into pieces that will fit into no more than m MB of memory, or into n
equal sized pieces. Each piece is computed sequentially, and the results are merged at the
end. Only one of -memory and -segments is needed.

-memorym
use at most m MB of memory per segment

-segmentsn
use n segments

Segmented,batchedoperation
Same as sequential, except this allows each segment to be manually executed in parallel.
Only one of -memory and -segments is needed. Also see the EXAMPLE section on this page.

-memorym
use at most m MB of memory per segment

-segmentsn
use n segments

-configbatch
create the batches

-countbatchn
run batch number n-mergebatch
merge the batches

Batched mode can run on the grid.

-sgejobname
unique job name for this execution. Meryl will submit jobs with name mpjobname,
ncjobname, nmjobname, for phases prepare, count and merge.

-sgebuild"options"-sgemerge"options"
any additional options to qsub(1) (e.g., "-p -153-pe thread 2 -A merylaccount")
N.B. - -N will be ignored N.B. - be sure to quote the options

-M Given a list of tables, perform a math, logical or threshold operation. Unless specified, all
operations take any number of databases. Math operations are:

min count is the minimum count for all databases. If the mer does NOT exist in all databases,
the mer has a zero count, and is NOT in the output.

minexist
count is the minimum count for all databases that contain the mer

max count is the maximum count for all databases

add count is sum of the counts for all databases

sub count is the first minus the second (binary only)

abs count is the absolute value of the first minus the second (binary only)

Logical operations are:

and outputs mer iff it exists in all databases

nand outputs mer iff it exists in at least one, but not all, databases

or outputs mer iff it exists in at least one database

xor outputs mer iff it exists in an odd number of databases

Threshold operations are:

lessthanx
outputs mer iff it has count < x

lessthanorequalx
outputs mer iff it has count <= x

greaterthanx
outputs mer iff it has count > x

greaterthanorequalx
outputs mer iff it has count >= x

equalx
outputs mer iff it has count == x

Threshold operations work on exactly one database.

-stblprefix
use tblprefix as a database

-otblprefix
create this output

-v entertain the user

-D Dump table (not all of these work)

-Dd Dump a histogram of the distance between the same mers.

-Dt Dump mers >= a threshold. Use -n to specify the threshold.

-Dc Count the number of mers, distinct mers and unique mers.

-Dh Dump (to stdout) a histogram of mer counts.

-s Read the count table from here (leave off the .mcdat or .mcidx).

Synopsis

Estimatingmemoryrequirementsmeryl-P-mkmersize [-c#] [-p] -sseq.fastameryl-P-mkmersize [-c#] [-p] -nmercountBuildingatablemeryl-B-mkmersize  [-c#]  [-p] [-v] [-f|-r|-C] [-Lminoccurrence] [-Umaxoccurrence] [-threadsn |
       {-segmentssegments | -memorymegabytes} [-configbatch [-sgejobname]]] -sseq.fasta-otblprefixmeryl-countbatchnumber [-sgebuild "qsuboptionstring"] -otblprefixmeryl-mergebatchnumber [-sgemerge "qsuboptionstring"] -otblprefixPerformingoperationsonatablemeryl-Moperation [-v] -stblprefix [-stblprefix2 ...]  -ooutputDumpingatablemeryl-Dh-stblprefixmeryl-Dt-nmincount-stblprefix