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- Overview
- Dependency
- Installing PECAT from source codes
- Installing third-party tools using conda
- Docker pre-built image
- Testing
- Quick Start
- Notes
- More details
PECAT is a phased error correction and assembly tool for long reads. It includes a haplotype-aware correction method and an efficient diploid assembly method.
•python3 (3.6+)
•minimap2 (2.17+)
•racon (v1.4.21+)
•perl (v5.22.1+)
•samtools (1.7+)
•clair3 (v0.1-r12+) (optional)
or
After building, all the executable files can be found in PECAT/build/bin. We can run PECAT/build/bin/pecal.pl or add the path to the system PATH and run pecal.pl.zlib not found
Installing and configuring clair3 and medaka
When we installed clair3 and medaka using conda, we encountered a conflict between clair3(v0.1-r12) and medaka (1.7.2). Only one of them can be installed. If you also fail to install the tools, we recommend using singularity or docker to invoke them.
There is a pre-built docker image. Use the following commands to run pecat.
•-v $CWD:/mnt: Map current working directory ($CWD) of the host to current working directory (/mnt) of the container, so PECAT can access the config file cfg.
•-v /var/run/docker.sock:/var/run/docker.sock: Docker in Docker. By adding this parameter, pecat in the container can run the docker images (clair3 and medaka) of the host.
•The directory of datasets should also be mapped carefully to ensure that PECAT in the container can access them.
Add the following parameters to the config file, so that pecat can call clair3 and medaka in the container.
•$CWD: should be set to an absolute path of current working directory in the host.
We can run the demo to test whether PECAT has been succesfully installed. See demo/README.md.
Create a config file using the following command,
Fill in the necessary parameters.
Run PECAT to assemble the reads.
•The corrected reads are in the file S1/1-correct/corrected_reads.fasta.
•The primary/alternate-format contigs are in the files S1/6-polish/racon/{primary.fasta,alternate.fasta}.
•The dual-format contigs are in the files S1/6-polish/racon/{haplotype_1.fasta,haplotype_2.fasta}.
Note: We strongly recommend setting the parameter cleanup=1. PECAT deletes temporary files, otherwise it take up a lot of disk space.
Note: For large genomes such as cattle and human, we strongly suggest adding the parameter -f 0.005 or -f 0.002 to corr_rd2rd_options and align_rd2rd_options. See cfg_cattle_clr, cfg_cattle_ont and cfg_hg002_ont. The parameter is passed to minimap2, which means to filter out top 0.005 or 0.002 fraction of repetitive minimizers. It outputs less candidate overlaps, which reduces disk usage and speeds up error correction step and assembling step.
PECAT follows the correct-then-assemble strategy, including an error correction module and a two-round string-graph-based assembly module. Here, we describe some important steps and parameters. See config.md
5. Apr. 2024 · Here, we present PECAT, a Phased Error Correction and Assembly Tool, for reconstructing diploid genomes from long noisy reads. We design a haplotype-aware error correction method that can retain...
Vor 4 Tagen · Pečat je najčitaniji magazin u Srbiji koji analizira društveno-političke i kulturne teme. Na Novinarnici možete kupiti e-izdanje, pretplatu ili čitati besplatan primerak Pečata.
19. Jan. 2024 · Јово Вуковић 24/11/2023 ПЕЧАТ НЕДЕЉЕ, БРОЈ 788 0. Најбољи фудбалери Србије ће, после 24 године, играти на шампионату Старог континента, а тенисер Ђоковић, победом на завршном мастерсу године ...
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