hicassembler
Software to assemble contigs/scaffolds into chromosomes using Hi-C data
Science Score: 23.0%
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Low similarity (12.4%) to scientific vocabulary
Repository
Software to assemble contigs/scaffolds into chromosomes using Hi-C data
Basic Info
- Host: GitHub
- Owner: maxplanck-ie
- Language: Python
- Default Branch: master
- Size: 8.31 MB
Statistics
- Stars: 29
- Watchers: 6
- Forks: 4
- Open Issues: 19
- Releases: 0
Metadata Files
README.md
HiCAssembler
Hi-C scaffolding tool to assemble contigs/scaffolds into complete chromosomes
This software uses Hi-C sequencing data to assemble contigs/scaffolds into complete chromosomes. The assembly process consists of the following steps:
- creation of corrected Hi-C contact matrix
- detection of mis-assemblies (automatic and/or manual)
- creation of initial path graph
- iterative joining of high-confidence scaffold paths
- addition of scaffolds that were not used yet
- saving of scaffolds fasta file and liftover chain file
HiCAssembler automatically visualizes the assembly process to inform the user on the assembly status
Installation
HiCAssembler works with python 2.7 and requires that HiCExplorer is installed
To install HiCAssembler use pip.
bash
$ pip install HiCAssembler
If you want to install the latest version use:
bash
$ pip install git+https://github.com/maxplanck-ie/HiCAssembler.git
[!WARNING] If you wanted to use a conda environment, create it with:
$ mamba create -n hicassembler python~=2.7 'setuptools<=41' 'pip<=21' 'biopython<=1.76' 'hic2cool<=0.8' 'numexpr<=2.7' 'pyBigWig>=0.3.10' 'hicexplorer>=2.1.1' 'cooler>=0.7.6' 'networkx>=2.1', and then you will be able to pip-install our tool.
Usage
Before running HiCAssembler, creation of a corrected Hi-C matrix in h5 format is required. This file format is the output created by HiCExporer (http://hicexplorer.readthedocs.io/). Hi-C reads need to be mapped to your pre-assembled contigs/scaffolds and then the Hi-C matrix needs to be created and corrected. An example usage of HiCExporer for these steps can be found at http://hicexplorer.readthedocs.io/en/latest/content/example_usage.html.
Afterwards, you can start to assemble your pre-assembled contigs/scaffolds into chromosomes using HiCAssembler.
bash
$ assemble -m Hi_C_matrix_corrected.h5 -o ./assembly_output \
--min_scaffold_length 100000 --bin_size 5000 --misassembly_zscore_threshold -1.0 \
--num_iterations 3 --num_processors 16
--min_scaffold_length 100000 sets the minimal length of pre-assembled scaffolds
to 100 kb. Scaffolds smaller than 100 kb are added after the iterative correction.
--bin_size 5000 sets the Hi-C bin size to 5 kb. This would be the size of
high-resolution bins referred to in the algorithm description.
--misassembly_zscore_threshold -1.0 sets the threshold deciding if a
TAD-separation score is strong enough to be considered a mis-assembly.
--num_iterations 3 sets the number of assembly iterations to 3.
In case your final result contains assembly errors, you can manually correct them.
The position of assembly errors can be specified and added as a position to
cut your pre-assembled contigs/scaffolds before the assembly using the
--split_positions_file split.bed parameter. The exact position of the error
in the pre-assembled contigs/scaffolds can be identified by using the tool
plotScaffoldInteractive.
bash
$ plotScaffoldInteractive scaffold_123
The position of the assembly error is displayed by moving your cursor over it.
Citation
Gina Renschler, Gautier Richard, Claudia Isabelle Keller Valsecchi, Sarah Toscano, Laura Arrigoni, Fidel Ramirez, Asifa Akhtar. "Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling", Genes & Development (2019), doi: https://doi.org/10.1101/gad.328971.119
Examples
(A small corrected Hi-C matrix can be found in the data/ folder)
A minimal example of the assembly of several scaffolds:
bash
$ assemble -m /data/hic_small.h5 -o ./assembly_output \
--min_scaffold_length 100000 --bin_size 5000 --misassembly_zscore_threshold -1.0 \
--num_iterations 3 --num_processors 16
Each step of the assembly is automatically visualized.
Now, let's see how scaffolds with and without mis-assemblies look like:
Assembly errors can easily be detected as an abrupt change in the Hi-C signal. HiCAssembler automatically splits scaffolds at minima of the Hi-C score as shown here:
Strong TAD boundaries with a low TAD-separation score can wrongly be considered as
mis-assemblies. The threshold of the score where scaffolds get split needs to
be chosen using the --misassembly_zscore_threshold parameter.
A balance between too many splits and thus very small scaffolds after splitting
and too many left-over mis-assemblies needs to be found. We identified a score
of -1 as a good starting point for assemblies but we recommend to test several
settings. Some scaffolds will be split at TAD boundaries. This is no problem
because they will be connected again by the assembly process afterwards.
If not all mis-assemblies are split automatically, splits can be added manually
using the --split_positions_file split.bed parameter. The exact position of
the error in the pre-assembled contigs/scaffolds can be identified by using the tool
plotScaffoldInteractive.
bash
$ plotScaffoldInteractive scaffold_123
The position of the assembly error is displayed by moving your cursor over it.
Owner
- Name: Max Planck Institute of Immunobiology and Epigenetics
- Login: maxplanck-ie
- Kind: organization
- Location: Freiburg, Germany
- Website: https://www.ie-freiburg.mpg.de/
- Repositories: 35
- Profile: https://github.com/maxplanck-ie
GitHub Events
Total
- Watch event: 1
Last Year
- Watch event: 1
Committers
Last synced: almost 3 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| fidelram | f****z@g****m | 126 |
| Fidel Ramirez | r****z@i****e | 57 |
| GinaRe | 3****e | 4 |
| Gina Renschler | r****r@i****e | 2 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 19
- Total pull requests: 6
- Average time to close issues: N/A
- Average time to close pull requests: 2 minutes
- Total issue authors: 16
- Total pull request authors: 1
- Average comments per issue: 2.58
- Average comments per pull request: 0.0
- Merged pull requests: 6
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 0.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- xinwang-bio (3)
- dominik-handler (2)
- yangxiaofeill (1)
- clauderispe (1)
- ddelgadillod (1)
- nadegeguiglielmoni (1)
- zhuangfjnu (1)
- ManuPoretti (1)
- zhanyinx (1)
- MartinLaforest (1)
- rob123king (1)
- karimi81 (1)
- gtrichard (1)
- yongyiyu (1)
- francicco (1)
Pull Request Authors
- fidelram (6)
Top Labels
Issue Labels
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Packages
- Total packages: 1
-
Total downloads:
- pypi 20 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 2
- Total maintainers: 1
pypi.org: hicassembler
Hi-C guided genome assembly
- Homepage: https://github.com/maxplanck-ie/HiCAssembler
- Documentation: https://hicassembler.readthedocs.io/
- License: BSD
-
Latest release: 1.1.1
published over 7 years ago
Rankings
Maintainers (1)
Dependencies
- cooler >=0.7.6
- future >=0.16.0
- hicexplorer >=2.1.1
- matplotlib >=2.0.0
- networkx >=2.1
- numpy >=1.13.1
- pyBigWig >=0.3.10
- pytest >=2.8.1
- versioneer >=0.18