dentist ~master

DENTIST

DENTIST uses long reads to close assembly gaps at high accuracy.

Long sequencing reads allow increasing contiguity and completeness of fragmented, short-read based genome assemblies by closing assembly gaps, ideally at high accuracy. DENTIST is a sensitive, highly-accurate and automated pipeline method to close gaps in (short read) assemblies with long reads.

API documentation: current, v4.0.0, v3.0.0, v2.0.0

First time here? Head over to [the example](#example) and make sure it works.

Table of Contents

• Install
• Usage
• Example
• Configuration
• Troubleshooting
• Citation
• Maintainer
• Contributing
• License

Install

Use Conda via Snakemake (recommended)

Make sure Mamba (a frontend for Conda) is installed on your system. You can then use DENTIST like so:

# run the whole workflow on a cluster using Conda
snakemake --configfile=snakemake.yml --use-conda -jall
snakemake --configfile=snakemake.yml --use-conda --profile=slurm

The last command is explained in more detail below in the usage section.

Note: If you do not have `mamba` installed, you may need to pass `--conda-frontend=conda` to Snakemake.

Use Conda to Manually Install Binaries

Make sure Mamba (a frontend for Conda) is installed on your system. Install DENTIST and all dependencies like so:

mamba create -n dentist -c a_ludi -c bioconda dentist-core
mamba activate dentist
mamba install -c conda-forge -c bioconda snakemake

# execute the workflow
snakemake --configfile=snakemake.yml --cores=all

More details on executing DENTIST can be found in the usage section.

Use Pre-Built Binaries

Download the latest pre-built binaries from the releases section and extract the contents. The pre-built binaries are stored in a subfolder called bin. Here are the instructions for v4.0.0:

# download & extract pre-built binaries
wget https://github.com/a-ludi/dentist/releases/download/v4.0.0/dentist.v4.0.0.x86_64.tar.gz
tar -xzf dentist.v4.0.0.x86_64.tar.gz

# make binaries available to your shell
cd dentist.v4.0.0.x86_64
PATH="$PWD/bin:$PATH"

# check installation with
dentist -d
# Expected output:
# 
#daligner (part of `DALIGNER`; see https://github.com/thegenemyers/DALIGNER) [OK]
#damapper (part of `DAMAPPER`; see https://github.com/thegenemyers/DAMAPPER) [OK]
#DAScover (part of `DASCRUBBER`; see https://github.com/thegenemyers/DASCRUBBER) [OK]
#DASqv (part of `DASCRUBBER`; see https://github.com/thegenemyers/DASCRUBBER) [OK]
#DBdump (part of `DAZZ_DB`; see https://github.com/thegenemyers/DAZZ_DB) [OK]
#DBdust (part of `DAZZ_DB`; see https://github.com/thegenemyers/DAZZ_DB) [OK]
#DBrm (part of `DAZZ_DB`; see https://github.com/thegenemyers/DAZZ_DB) [OK]
#DBshow (part of `DAZZ_DB`; see https://github.com/thegenemyers/DAZZ_DB) [OK]
#DBsplit (part of `DAZZ_DB`; see https://github.com/thegenemyers/DAZZ_DB) [OK]
#fasta2DAM (part of `DAZZ_DB`; see https://github.com/thegenemyers/DAZZ_DB) [OK]
#fasta2DB (part of `DAZZ_DB`; see https://github.com/thegenemyers/DAZZ_DB) [OK]
#computeintrinsicqv (part of `daccord`; see https://gitlab.com/german.tischler/daccord) [OK]
#daccord (part of `daccord`; see https://gitlab.com/german.tischler/daccord) [OK]

The tarball additionally contains the Snakemake workflow, example config files and this README. In short, everything you to run DENTIST.

Use a Singularity Container (discouraged)

Remark: the Singularity container may not work properly depending on your system. (see issue #30)

Make sure Singularity is installed on your system. You can then use the container like so:

# launch an interactive shell
singularity shell docker://aludi/dentist:stable

# execute a single command inside the container
singularity exec docker://aludi/dentist:stable dentist --version

# run the whole workflow on a cluster using Singularity
snakemake --configfile=snakemake.yml --use-singularity --profile=slurm

The last command is explained in more detail below in the usage section.

Build from Source

1. Install the D package manager DUB.
2. Install JQ 1.6.
3. Build DENTIST using either

   dub install dentist
   

   or

   git clone --recurse-submodules https://github.com/a-ludi/dentist.git
   cd dentist
   dub build
   

Runtime Dependencies

The following software packages are required to run dentist:

• The Dazzler Data Base (>=2020-07-27)

Manage sequences (reads and assemblies) in 4bit encoding alongside auxiliary information such as masks or QV tracks

• DALIGNER (=2020-01-15)

Find significant local alignments.

• DAMAPPER (>=2020-03-22)

Find alignment chains, i.e. sequences of significant local alignments possibly with unaligned gaps.

• DAMASKER (>=2020-01-15)

Discover tandem repeats.

• DASCRUBBER (>=2020-07-26)

Estimate coverage and compute QVs.

• daccord (>=v0.0.18)

Compute reference-based consensus sequence for gap filling.

Please see their own documentation for installation instructions. Note, the available packages on Bioconda are outdated and should not be used at the moment but they are available using conda install -c a_ludi <dependency>.

Please use the exact versions specified in the Conda recipe in case you experience troubles.

Usage

Before you start producing wonderful scientific results, you should skip over to the example section and try to run the small example. This will make sure your setup is working as expected.

Quick execution with Snakemake

TL;DR

wget https://github.com/a-ludi/dentist/releases/download/v4.0.0/dentist.v4.0.0.x86_64.tar.gz
tar -xzf dentist.v4.0.0.x86_64.tar.gz
cd dentist.v4.0.0.x86_64

# edit dentist.yml and snakemake.yml

# execute with CONDA:
snakemake --configfile=snakemake.yml --use-conda

# execute with SINGULARITY:
snakemake --configfile=snakemake.yml --use-singularity

# execute with pre-built binaries:
PATH="$PWD/bin:$PATH" snakemake --configfile=snakemake.yml

Install Snakemake version >=5.32.1 and prepare your working directory:

wget https://github.com/a-ludi/dentist/releases/download/v4.0.0/dentist.v4.0.0.x86_64.tar.gz
tar -xzf dentist.v4.0.0.x86_64.tar.gz

cp -r -t . \
    dentist.v4.0.0.x86_64/snakemake/dentist.yml \
    dentist.v4.0.0.x86_64/snakemake/Snakefile \
    dentist.v4.0.0.x86_64/snakemake/snakemake.yml \
    dentist.v4.0.0.x86_64/snakemake/envs \
    dentist.v4.0.0.x86_64/snakemake/scripts

Next edit snakemake.yml and dentist.yml to fit your needs and optionally test your configuration with

# see above for variants with pre-built binaries or Singularity
snakemake --configfile=snakemake.yml --use-conda --cores=1 -f -- validate_dentist_config

If no errors occurred the whole workflow can be executed using

# see above for variants with pre-built binaries or Singularity
snakemake --configfile=snakemake.yml --use-conda --cores=all

For small genomes of a few 100 Mbp this should run on a regular workstation. One may use Snakemake's --cores to run independent jobs in parallel. Larger data sets may require a cluster in which case you can use Snakemake's cloud or cluster facilities.

Executing on a Cluster

Please follow the setup steps from above except for the actual execution.

To make execution on a cluster easy DENTIST comes with examples files to make Snakemake use SLURM via DRMAA, sbatch or srun found under snakemake. If your cluster does not use SLURM please modify the profiles to suit your needs or read the documentation of Snakemake. Another good starting point is the Snakemake-Profiles project.

After you have selected an appropriate cluster profile, make it available to Snakemake, e.g.:

# choose appropriate file from `snakemake/profile-slurm.*.yml`
mkdir -p ~/.config/snakemake/slurm
cp ./snakemake/profile-slurm.submit-async.yml ~/.config/snakemake/slurm/config.yaml

Adjust the profile according to your cluster, e.g. you may need to specify accounting information. Values defined in cluster.yml can be used in the profile as demonstrated in the examples. This file is also the place to modify resource allocations and job names.

Now, you can execute the workflow like this:

snakemake --configfile=snakemake.yml --profile=slurm --use-conda

Snakemake will now start submitting jobs to your cluster until all the work is done. If something fails, you can execute the same command again to continue from the latest state of the workflow.

Manual execution

Please inspect the Snakemake workflow to get all the details. It might be useful to execute Snakemake with the -p switch which causes Snakemake to print the shell commands. If you plan to write your own workflow management for DENTIST please feel free to contact the maintainer!

Example

Make sure you have Snakemake 5.32.1 or later installed.

You can also use the convenient Conda package to execute the rules. Just make sure you have Mamba installed.

First of all download the test data and workflow and switch to the dentist-example directory.

wget https://github.com/a-ludi/dentist/releases/download/v4.0.0/dentist-example.tar.gz
tar -xzf dentist-example.tar.gz
cd dentist-example

Local Execution

Execute the entire workflow on your local machine using all cores:

# run the workflow
PATH="$PWD/bin:$PATH" snakemake --configfile=snakemake.yml --cores=all

# validate the files
md5sum -c checksum.md5

Execution takes approx. 7 minutes and a maximum of 1.7GB memory on my little laptop with an Intel® Core™ i5-5200U CPU @ 2.20GHz.

Execution with Conda

Make sure Mamba (a frontend for Conda) is installed on your system. Execute the workflow without explicit installation by adding --use-conda to the call to Snakemake:

# run the workflow
snakemake --configfile=snakemake.yml --use-conda --cores=all

# validate the files
md5sum -c checksum.md5

Note: If you do not have `mamba` installed, you may need to pass `--conda-frontend=conda` to Snakemake.

Execution in Singularity Container (discouraged)

Remark: the Singularity container may not work properly depending on your system. (see issue #30)

Execute the workflow inside a convenient Singularity image by adding --use-singularity to the call to Snakemake:

# run the workflow
snakemake --configfile=snakemake.yml --use-singularity --cores=all

# validate the files
md5sum -c checksum.md5

Cluster Execution

Please follow the instructions "Executing on a Cluster" above.

Configuration

DENTIST comprises a complex pipeline of with many options for tweaking. This section points out some important parameters and their effect on the result or performance.

The default parameters are rather conservative, i.e. they focus on correctness of the result while not sacrificing too much sensitivity.

We also provide a greedy sample configuration (snakemake/dentist.greedy.yml) which focuses on sensitivity but may introduce more errors. **Warning:** Use with care! Always validate the closed gaps (e.g. manual inspection).

In any case, the workflow creates an intermediate assembly workdir/{output_assembly}-preliminary.fasta that contains all closed gaps, i.e. before validation. It is accompanied by an AGP and BED file. You may inspect these file for maximum sensitivity.

How to Choose DENTIST Parameters

While the list of all commandline parameters is a good reference, it does not provide an overview of the important parameters. Therefore, we provide this shorter list of important and influential parameters. Please also consider adjusting the performance parameter in the workflow configuration (snakemake/snakemake.yml).

• --read-coverage: This is the preferred way of providing values to --max-coverage-reads, --max-improper-coverage-reads and --min-coverage-reads. See below how their values are derived from --read-coverage.

  Ideally, the user provides the haploid read coverage which, can be inferred using a histogram of the alignment coverage across the assembly. Alternatively, the average raw read coverage can be used which is the number of base pairs in the reads divided by the number of base pairs in the assembly.

• --ploidy: Combined with --read-coverage, this parameters is the preferred way of providing --min-coverage-reads.

  We use the Wikipedia definition of ploidy, as "the number of complete sets of chromosomes in a cell" (https://en.wikipedia.org/wiki/Ploidy)

• --max-coverage-reads, --max-improper-coverage-reads: These parameters are used to derive a repeat mask from the ref vs. reads alignment. If the coverage of (improper) alignments is larger than the given theshold it will be considered repetitive. If supplied, default values are derived from --read-coverage as follows:

  The maximum read coverage C_max is calculated from the global read coverage C (provided via --read-coverage) such that the probability of observing more than C_max alignments in a unique (non-repetitive) genomic region is very small (see paper, Methods section and Supplementary Table 2). In practice, this probability is approximated via

  C_max = floor(C / log(log(log(b * C + c) / log(a))))
  where
      a = 1.65
      b = 0.1650612
      c = 5.9354533
  

  To further increase the sensitivity, DENTIST searches for smaller repeat-induced local alignments. To this end, we define an alignment as proper if there are at most 100 bp (adjustable via --proper-alignment-allowance) of unaligned sequence on either end of the read. All other alignments, where only a smaller substring of the read aligns, are called improper. Improper alignments are often indicative of repetitive regions. Therefore, DENTIST considers genomic regions, where the number of improper read alignments is higher than a threshold to be repetitive. By default, this threshold equals half the global read coverage C. (see paper, Methods section). In practice, a smoothed version of max(4, x/2) is used to provide better performance for very low read coverage. The maximum improper read coverage I_max is computed as

  I_max = floor(a*x + exp(b*(c - x)))
  where
      a = 0.5
      b = 0.1875
      c = 8
  

• --dust-{reads,ref}, --daligner-{consensus,reads-vs-reads,self}, --damapper-ref-vs-reads, --datander-ref, --daccord: These options allow passing parameters to the respective tools. They may have dramatic influence on the result. The default settings work well for PacBio CLR reads and should also work well with raw Nanopore data.

  In-depth discussion of each tool goes beyond the scope of this document, please refer to the respective documentations (DBdust, daligner, damapper, datander, daccord).

• --max-insertion-error: Strong influence on quality and sensitivity. Lower values lead to lower sensitivity but higher quality. The maximum recommended value is 0.05.
• --min-anchor-length: Higher values results in higher accuracy but lower sensitivity. Especially, large gaps cannot be closed if the value is too high. Usually the value should be at least 500 and up to 10_000.
• --min-reads-per-pile-up: Choosing higher values for the minimum number of reads drastically reduces sensitivity but has little effect on the quality. Small values may be chosen to get the maximum sensitivity in de novo assemblies. Make sure to throughly validate the results though.
• --min-spanning-reads: Higher values give more confidence on the correctness of closed gaps but reduce sensitivity. The value must be well below the expected coverage.
• --allow-single-reads: May be used under careful consideration in combination with --min-spanning-reads=1. This is intended for one of the following scenarios:
  1. DENTIST is meant to close as many gaps as possible in a de novo assembly. Then the closed gaps must be validated by other means afterwards.
  2. DENTIST is used not with real reads but with an independent assembly.
• --existing-gap-bonus: If DENTIST finds evidence to join two contigs that are already consecutive in the input assembly (i.e. joined by Ns) then it will preferred over conflicting joins (if present) with this bonus. The default value is rather conservative, i.e. the preferred join almost always wins over other joins in case of a conflict.
• --join-policy: Choose according to your needs:
  • scaffoldGaps: Closes only gaps that are marked by Ns in the assembly. This is the default mode of operation. Use this if you do not want to alter the scaffolding of the assembly. See also --existing-gap-bonus.
  • scaffolds: Allows whole scaffolds to be joined in addition to the effects of scaffoldGaps. Use this if you have (many) scaffolds that are not yet full chromosome-scale.
  • contigs: Allows contigs to be rearranged freely. This is especially useful in de novo assemblies before applying any other scaffolding methods as it increases the contiguity thus increasing the chance that large-scale scaffolding (e.g. Bionano or Hi-C) finds proper joins.
• --min-coverage-reads, --min-spanning-reads, --region-context: DENTIST validates closed gaps by mapping the reads to the gap-closed assembly. It requires for each gap and the base pairs down- and upstream (--region-context) are (1) covered by at least --min-coverage-reads reads at every position and (2) are spanned by at least --min-spanning-reads reads. Thus, increasing any of these numbers makes the valid gaps more robust but may reduce their number.

  If --min-coverage-reads is not provided, it will be derived from --read-coverage (see above) and --ploidy. Given (haploid) read coverage C and ploidy p, the minimum read coverage C_min is calculated as

    C_min = C / (2 * p)
  

  This corresponds to 50% of the long read coverage expected to be sequenced from a haploid locus (see paper, Methods section).

Choosing the Read Type

In the examples PacBio long reads are assumed but DENTIST can be run using any kind of long reads. Currently, this is either PacBio or Oxford Nanopore reads. For using none-PacBio reads, the reads_type in snakemake.yml must be set to anything other than PACBIO_SMRT. The recommendation is to use OXFORD_NANOPORE for Oxford Nanopore. These names are borrowed from the NCBI. Further details on the rationale can found in this issue.

Cluster/Cloud Execution

Cluster job schedulers can become unresponsive or even crash if too many jobs with short running time are submitted to the cluster. It is therefore advisable to adjust the workflow accordingly. We tried to provide a default configuration that works in most cases as is but the application scenarios can be very diverse and manual adjustments may become necessary. Here is a small guide which config parameters influence the number of jobs and how much resources they consume.

• threads_per_process: Sets the maximum number of threads/cores a single job may use. A single-threaded job will always allocate a single core but thread-parallel steps, e.g. the sequence alignments, will use up to threads_per_process if snakemake has been provided enough cores via --cores.
• -s<block_size:uint>: The assembly and reads FAST/A files are converted into Dazzler DBs. These DBs store the sequence in a 2-bit encoding and have additional features like tracks (similar to BED files). Also they are split into blocks of <block_size>Mb. Alignments are calculated on the basis of these blocks which enables easy distribution onto the cluster. The larger the block size the longer are the alignment jobs and the more memory they require but also the number of jobs is reduced. Experience shows that the block size should be between 200Mb and 500Mb.
• propagate_batch_size: The repeat masks are homogenized by propagating them from the assembly to the reads and back again. Usually these jobs are very short because the propagation is parallelized over the blocks of the reads DB. To reduce the number of jobs both propagation directions are grouped together and submitted in batches of propagate_batch_size read blocks. Increasing propagate_batch_size reduces the number of submitted jobs and increases the run time per job. It has no effect on the memory requirements.
• batch_size: In the collect step DENTIST identifies candidates for gap closing each consisting of a pile up of reads. From these pile ups consensus sequences are computed and validated in the process step. Each job process batch_size pile ups. Increasing batch_size reduces the number of submitted jobs and increases the run time per job. It has no effect on the memory requirements.
• validation_blocks: The preliminarily closed gaps are validated by analyzing how the reads align to each closed gap. The validation is conducted in independent jobs for validation_blocks many blocks of the gap-closed assembly. Decreasing validation_blocks reduces the number of submitted jobs and increases the run time and memory requirements per job. The memory requirement is proportional to the size of the read alignment blocks.

Troubleshooting

Regular ProtectedOutputException

Snakemake has a built-in facility to protect files from accidental overwrites. This is meant to avoid overwriting precious results that took many CPU hours to produce. If executing a rule would overwrite a protected file, Snakemake raises a ProtectedOutputException, e.g.:

ProtectedOutputException in line 1236 of /tmp/dentist-example/Snakefile:
Write-protected output files for rule collect:
workdir/pile-ups.db
  File "/usr/lib/python3.9/site-packages/snakemake/executors/__init__.py", line 136, in run_jobs
  File "/usr/lib/python3.9/site-packages/snakemake/executors/__init__.py", line 441, in run
  File "/usr/lib/python3.9/site-packages/snakemake/executors/__init__.py", line 230, in _run
  File "/usr/lib/python3.9/site-packages/snakemake/executors/__init__.py", line 155, in _run

Here workdir/pile-ups.db is the protected file that caused the error. If you are sure of what you are doing, you can simply raise the protection by chmod -R +w ./workdir and execute Snakemake again. Now, it will overwrite any files.

No internet connection on compute nodes

If you have no internet connection on your compute nodes or even the cluster head node and want to use Singularity for execution, you will need to download the container image manually and put it to a location accessible by all jobs. Assume /path/to/dir is such a location on your cluster. Then download the container image using

# IF internet connection on head node
singularity pull --dir /path/to/dir docker://aludi/dentist:stable

# ELSE (on local machine)
singularity pull docker://aludi/dentist:stable
# copy dentist_stable.sif to cluster
scp dentist_stable.sif cluster:/path/to/dir/dentist_stable.sif

When the image is in place you will need to adjust your configuration in snakemake.yml:

dentist_container: "/path/to/dir/dentist_stable.sif"

Now, you are ready for execution.

Note, if you want to use Conda without internet connection, you can just use the pre-compiled binaries instead because they are just what Conda will install. Be sure to adjust your PATH accordingly, e.g.:

PATH="$PWD/bin:$PATH" snakemake --configfile=snakemake.yml --profile=slurm

Illegally formatted line from DBshow -n

This error message may appear in DENTIST's log files. It is a known bug that will be fixed in a future release. In the meantime avoid FASTA headers that contain a literal " :: ".

Citation

Arne Ludwig, Martin Pippel, Gene Myers, Michael Hiller. DENTIST — using long reads for closing assembly gaps at high accuracy. GigaScience, Volume 11, 2022, giab100. https://doi.org/10.1093/gigascience/giab100

Maintainer

DENTIST is being developed by Arne Ludwig <ludwig@mpi-cbg.de> at the Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.

Contributing

Contributions are warmly welcome. Just create an issue or pull request on GitHub. If you submit a pull request please make sure that:

• the code compiles on Linux using the current release of dmd,
• your code is covered with unit tests (if feasible) and
• dub test runs successfully.

It is recommended to install the Git hooks included in the repository to avoid premature pull requests. You can enable all shipped hooks with this command:

git config --local core.hooksPath .githooks/

If you do not want to enable just a subset use ln -s .githooks/{hook} .git/hooks. If you want to audit code changes before they get executed on your machine you can you cp .githooks/{hook} .git/hooks instead.

License

This project is licensed under MIT License (see LICENSE).