Canu Tutorial

Canu assembles reads from PacBio RS II or Oxford Nanopore MinION instruments into uniquely-assemblable contigs, unitigs. Canu owes lots of it design and code to celera-assembler.

Canu can be run using hardware of nearly any shape or size, anywhere from laptops to computational grids with thousands of nodes. Obviouisly, larger assemblies will take a long time to compute on laptops, and smaller assemblies can’t take advantage of hundreds of nodes, so what is being assembled plays some part in determining what hardware can be effectively used.

Most algorithms in canu have been multi-threaded (to use all the cores on a single node), parallelized (to use all the nodes in a grid), or both (all the cores on all the nodes).

Canu, the command

The canu command is the ‘executive’ program that runs all modules of the assembler. It oversees each of the three top-level tasks (correction, trimming, unitig construction), each of which consists of many steps. Canu ensures that input files for each step exist, that each step successfully finished, and that the output for each step exists. It does minor bits of processing, such as reformatting files, but generally just executes other programs.

canu [-correct | -trim | -assemble | -trim-assemble] \
  [-s <assembly-specifications-file>] \
   -p <assembly-prefix> \
   -d <assembly-directory> \
   genomeSize=<number>[g|m|k] \
   [other-options] \
   [-pacbio-raw | -pacbio-corrected | -nanopore-raw | -nanopore-corrected] *fastq

The -p option, to set the file name prefix of intermediate and output files, is mandatory. If -d is not supplied, canu will run in the current directory, otherwise, Canu will create the assembly-directory and run in that directory. It is _not_ possible to run two different assemblies in the same directory.

The -s option will import a list of parameters from the supplied specification (‘spec’) file. These parameters will be applied before any from the command line are used, providing a method for setting commonly used parameters, but overriding them for specific assemblies.

By default, all three top-level tasks are performed. It is possible to run exactly one task by using the -correct, -trim or -assemble options. These options can be useful if you want to correct reads once and try many different assemblies. We do exactly that in the Canu Quick Start. Additionally, suppling pre-corrected reads with -pacbio-corrected or -nanopore-corrected will run only the trimming (-trim) and assembling (-assemble) stages.

Parameters are key=value pairs that configure the assembler. They set run time parameters (e.g., memory, threads, grid), algorithmic parameters (e.g., error rates, trimming aggressiveness), and enable or disable entire processing steps (e.g., don’t correct errors, don’t search for subreads). They are described later. One parameter is required: the genomeSize (in bases, with common SI prefixes allowed, for example, 4.7m or 2.8g; see genomeSize). Parameters are listed in the Canu Parameter Reference, but the common ones are described in this document.

Reads are supplied to canu by options that options that describe how the reads were generated, and what level of quality they are, for example, -pacbio-raw indicates the reads were generated on a PacBio RS II instrument, and have had no processing done to them. Each file of reads supplied this way becomes a ‘library’ of reads. The reads should have been (physically) generated all at the same time using the same steps, but perhaps sequenced in multiple batches. In canu, each library has a set of options setting various algorithmic parameters, for example, how aggressively to trim. To explicitly set library parameters, a text ‘gkp’ file describing the library and the input files must be created. Don’t worry too much about this yet, it’s an advanced feature, fully described in Section gkp-files.

The read-files contain sequence data in either FASTA or FASTQ format (or both! A quirk of the implementation allows files that contain both FASTA and FASTQ format reads). The files can be uncompressed, gzip, bzip2 or xz compressed. We’ve found that “gzip -1” provides good compression that is fast to both compress and decompress. For ‘archival’ purposes, we use “xz -9”.

Canu, the pipeline

The canu pipeline, that is, what it actually computes, comprises of computing overlaps and processing the overlaps to some result. Each of the three tasks (read correction, read trimming and unitig construction) follow the same pattern:

  • Load reads into the read database, gkpStore.
  • Compute k-mer counts in preparation for the overlap computation.
  • Compute overlaps.
  • Load overlaps into the overlap database, ovlStore.
  • Do something interesting with the reads and overlaps.
    • The read correction task will replace the original noisy read sequences with consensus sequences computed from overlapping reads.
    • The read trimming task will use overlapping reads to decide what regions of each read are high-quality sequence, and what regions should be trimmed. After trimming, the single largest high-quality chunk of sequence is retained.
    • The unitig construction task finds sets of overlaps that are consistent, and uses those to place reads into a multialignment layout. The layout is then used to generate a consensus sequence for the unitig.

Module Tags

Because each of the three tasks share common algorithms (all compute overlaps, two compute consensus sequences, etc), parameters are differentiated by a short prefix ‘tag’ string. This lets canu have one generic parameter that can be set to different values for each stage in each task. For example, “corOvlMemory” will set memory usage for overlaps being generated for read correction; “obtOvlMemory” for overlaps generated for Overlap Based Trimming; “utgOvlMemory” for overlaps generated for unitig construction.

The tags are:

Tag Usage
master the canu script itself, and any components that it runs directly
   
cns unitig consensus generation
cor read correction generation
   
red read error detection
oea overlap error adjustment
   
ovl the standard overlapper
corovl the standard overlapper, as used in the correction phase
obtovl the standard overlapper, as used in the trimming phase
utgovl the standard overlapper, as used in the assembly phase
   
mhap the mhap overlapper
cormhap the mhap overlapper, as used in the correction phase
obtmhap the mhap overlapper, as used in the trimming phase
utgmhap the mhap overlapper, as used in the assembly phase
   
mmap the minimap overlapper
cormmap the minimap overlapper, as used in the correction phase
obtmmap the minimap overlapper, as used in the trimming phase
utgmmap the minimap overlapper, as used in the assembly phase
   
ovb the bucketizing phase of overlap store building
ovs the sort phase of overlap store building

We’ll get to the details eventually.

Execution Configuration

There are two modes that canu runs in: locally, using just one machine, or grid-enabled, using multiple hosts managed by a grid engine. LSF, PBS/Torque, PBSPro, Sun Grid Engine (and derivations), and Slurm are supported, though LSF has has limited testing. Section Grid Engine Configuration has a few hints on how to set up a new grid engine.

By default, if a grid is detected the canu pipeline will immediately submit itself to the grid and run entirely under grid control. If no grid is detected, or if option useGrid=false is set, canu will run on the local machine.

In both cases, Canu will auto-detect available resources and configure job sizes based on the resources and genome size you’re assembling. Thus, most users should be able to run the command without modifying the defaults. Some advanced options are outlined below. Each stage has the same five configuration options, and tags are used to specialize the option to a specific stage. The options are:

useGrid<tag>=boolean
Run this stage on the grid, usually in parallel.
gridOptions<tag>=string
Supply this string to the grid submit command.
<tag>Memory=integer
Use this many gigabytes of memory, per process.
<tag>Threads
Use this many compute threads per process.
<tag>Concurrency
If not on the grid, run this many jobs at the same time.

Global grid options, applied to every job submitted to the grid, can be set with ‘gridOptions’. This can be used to add accounting information or access credentials.

A name can be associated with this compute using ‘gridOptionsJobName’. Canu will work just fine with no name set, but if multiple canu assemblies are running at the same time, they will tend to wait for each others jobs to finish. For example, if two assemblies are running, at some point both will have overlap jobs running. Each assembly will be waiting for all jobs named ‘ovl_asm’ to finish. Had the assemblies specified job names, gridOptionsJobName=apple and gridOptionsJobName=orange, then one would be waiting for jobs named ‘ovl_asm_apple’, and the other would be waiting for jobs named ‘ovl_asm_orange’.

Error Rates

Canu expects all error rates to be reported as fraction error, not as percent error. We’re not sure exactly why this is so. Previously, it used a mix of fraction error and percent error (or both!), and was a little confusing. Here’s a handy table you can print out that converts between fraction error and percent error. Not all values are shown (it’d be quite a large table) but we have every confidence you can figure out the missing values:

Fraction Error Percent Error
0.01 1%
0.02 2%
0.03 3%
. .
. .
0.12 12%
. .
. .

Canu error rates always refer to the percent difference in an alignment of two reads, not the percent error in a single read, and not the amount of variation in your reads. These error rates are used in two different ways: they are used to limit what overlaps are generated, e.g., don’t compute overlaps that have more than 5% difference; and they are used to tell algorithms what overlaps to use, e.g., even though overlaps were computed to 5% difference, don’t trust any above 3% difference.

There are seven error rates. Three error rates control overlap creation (corOvlErrorRate, obtOvlErrorRate and utgOvlErrorRate), and four error rates control algorithms (corErrorRate, obtErrorRate, utgErrorRate, cnsErrorRate).

The three error rates for overlap creation apply to the ovl overlap algorithm and the mhapReAlign option used to generate alignments from mhap or minimap overlaps. Since mhap is used for generating correction overlaps, the corOvlErrorRate parameter is not used by default. Overlaps for trimming and assembling use the ovl algorithm, therefore, obtOvlErrorRate and utgOvlErrorRate are used.

The four algoriothm error rates are used to select which overlaps can be used for correcting reads (corErrorRate); which overlaps can be used for trimming reads (obtErrorRate); which overlaps can be used for assembling reads (utgErrorRate). The last error rate, cnsErrorRate, tells the consensus algorithm to not trust read alignments above that value.

For convenience, two meta options set the error rates used with uncorrected reads (rawErrorRate) or used with corrected reads. (correctedErrorRate). The default depends on the type of read being assembled.

Parameter PacBio Nanopore
rawErrorRate 0.300 0.500
correctedErrorRate 0.045 0.144

In practice, only correctedErrorRate is usually changed. The Canu FAQ has specific suggestions on when to change this.

Canu v1.4 and earlier used the errorRate parameter, which set the expected rate of error in a single corrected read.

Minimum Lengths

Two minimum sizes are known:

minReadLength
Discard reads shorter than this when loading into the assembler, and when trimming reads.
minOverlapLength
Do not save overlaps shorter than this.

Overlap configuration

The largest compute of the assembler is also the most complicated to configure. As shown in the ‘module tags’ section, there are up to eight (!) different overlapper configurations. For each overlapper (‘ovl’ or ‘mhap’) there is a global configuration, and three specializations that apply to each stage in the pipeline (correction, trimming or assembly).

Like with ‘grid configuration’, overlap configuration uses a ‘tag’ prefix applied to each option. The tags in this instance are ‘cor’, ‘obt’ and ‘utg’.

For example:

  • To change the k-mer size for all instances of the ovl overlapper, ‘merSize=23’ would be used.
  • To change the k-mer size for just the ovl overlapper used during correction, ‘corMerSize=16’ would be used.
  • To change the mhap k-mer size for all instances, ‘mhapMerSize=18’ would be used.
  • To change the mhap k-mer size just during correction, ‘corMhapMerSize=15’ would be used.
  • To use minimap for overlap computation just during correction, ‘corOverlapper=minimap’ would be used.

Ovl Overlapper Configuration

<tag>Overlapper
select the overlap algorithm to use, ‘ovl’ or ‘mhap’.

Ovl Overlapper Parameters

<tag>ovlHashBlockLength
how many bases to reads to include in the hash table; directly controls process size
<tag>ovlRefBlockSize
how many reads to compute overlaps for in one process; directly controls process time
<tag>ovlRefBlockLength
same, but use ‘bases in reads’ instead of ‘number of reads’
<tag>ovlHashBits
size of the hash table (SHOULD BE REMOVED AND COMPUTED, MAYBE TWO PASS)
<tag>ovlHashLoad
how much to fill the hash table before computing overlaps (SHOULD BE REMOVED)
<tag>ovlMerSize
size of kmer seed; smaller - more sensitive, but slower

The overlapper will not use frequent kmers to seed overlaps. These are computed by the ‘meryl’ program, and can be selected in one of three ways.

Terminology. A k-mer is a contiguous sequence of k bases. The read ‘ACTTA’ has two 4-mers: ACTT and CTTA. To account for reverse-complement sequence, a ‘canonical kmer’ is the lexicographically smaller of the forward and reverse-complemented kmer sequence. Kmer ACTT, with reverse complement AAGT, has a canonical kmer AAGT. Kmer CTTA, reverse-complement TAAG, has canonical kmer CTTA.

A ‘distinct’ kmer is the kmer sequence with no count associated with it. A ‘total’ kmer (for lack of a better term) is the kmer with its count. The sequence TCGTTTTTTTCGTCG has 12 ‘total’ 4-mers and 8 ‘distinct’ kmers.

TCGTTTTTTTCGTCG  count
TCGT             2 distinct-1
 CGTT            1 distinct-2
  GTTT           1 distinct-3
   TTTT          4 distinct-4
    TTTT         4 copy of distinct-4
     TTTT        4 copy of distinct-4
      TTTT       4 copy of distinct-4
       TTTC      1 distinct-5
        TTCG     1 distinct-6
         TCGT    2 copy of distinct-1
          CGTC   1 distinct-7
           GTCG  1 distinct-8
<tag>MerThreshold
any kmer with count higher than N is not used
<tag>MerDistinct
pick a threshold so as to seed overlaps using this fraction of all distinct kmers in the input. In the example above, fraction 0.875 of the k-mers (7/8) will be at or below threshold 2.
<tag>MerTotal
pick a threshold so as to seed overlaps using this fraction of all kmers in the input. In the example above, fraction 0.667 of the k-mers (8/12) will be at or below threshold 2.
<tag>FrequentMers
don’t compute frequent kmers, use those listed in this fasta file

Mhap Overlapper Parameters

<tag>MhapBlockSize
Chunk of reads that can fit into 1GB of memory. Combined with memory to compute the size of chunk the reads are split into.
<tag>MhapMerSize
Use k-mers of this size for detecting overlaps.
<tag>ReAlign
After computing overlaps with mhap, compute a sequence alignment for each overlap.
<tag>MhapSensitivity
Either ‘normal’, ‘high’, or ‘fast’.

Mhap also will down-weight frequent kmers (using tf-idf), but it’s selection of frequent is not exposed.

Minimap Overlapper Parameters

<tag>MMapBlockSize
Chunk of reads that can fit into 1GB of memory. Combined with memory to compute the size of chunk the reads are split into.
<tag>MMapMerSize
Use k-mers of this size for detecting overlaps

Minimap also will ignore high-frequency minimzers, but it’s selection of frequent is not exposed.

Outputs

As Canu runs, it outputs status messages, execution logs, and some analysis to the console. Most of the analysis is captured in <prefix>.report as well.

LOGGING

<prefix>.report
Most of the analysis reported during assembly.

READS

<prefix>.correctedReads.fasta.gz
The reads after correction.
<prefix>.trimmedReads.fasta.gz
The corrected reads after overlap based trimming.

SEQUENCE

<prefix>.contigs.fasta
Everything which could be assembled and is part of the primary assembly, including both unique and repetitive elements.
<prefix>.unitigs.fasta
Contigs, split at alternate paths in the graph.
<prefix>.unassembled.fasta
Reads and low-coverage contigs which could not be incorporated into the primary assembly.

The header line for each sequence provides some metadata on the sequence.:

>tig######## len=<integer> reads=<integer> covStat=<float> gappedBases=<yes|no> class=<contig|bubble|unassm> suggestRepeat=<yes|no> suggestCircular=<yes|no>

len
   Length of the sequence, in bp.

reads
   Number of reads used to form the contig.

covStat
   The log of the ratio of the contig being unique versus being two-copy, based on the read arrival rate.  Positive values indicate more likely to be unique, while negative values indicate more likely to be repetitive.  See `Footnote 24 <http://science.sciencemag.org/content/287/5461/2196.full#ref-24>`_ in `Myers et al., A Whole-Genome Assembly of Drosophila <http://science.sciencemag.org/content/287/5461/2196.full>`_.

gappedBases
   If yes, the sequence includes all gaps in the multialignment.

class
   Type of sequence.  Unassembled sequences are primarily low-coverage sequences spanned by a single read.

suggestRepeat
   If yes, sequence was detected as a repeat based on graph topology or read overlaps to other sequences.

suggestCircular
   If yes, sequence is likely circular.  Not implemented.

GRAPHS

<prefix>.contigs.gfa
Unused or ambiguous edges between contig sequences. Bubble edges cannot be represented in this format.
<prefix>.unitigs.gfa
Contigs split at bubble intersections.
<prefix>.unitigs.bed
The position of each unitig in a contig.

METADATA

The layout provides information on where each read ended up in the final assembly, including contig and positions. It also includes the consensus sequence for each contig.

<prefix>.contigs.layout, <prefix>.unitigs.layout
(undocumented)
<prefix>.contigs.layout.readToTig, <prefix>.unitigs.layout.readToTig
The position of each read in a contig (unitig).
<prefix>.contigs.layout.tigInfo, <prefix>.unitigs.layout.tigInfo
A list of the contigs (unitigs), lengths, coverage, number of reads and other metadata. Essentially the same information provided in the FASTA header line.