Purge retained haplotypes using Purge-Dups
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This snakemake pipeline is designed to be run using as input a contig-level genome and pacbio reads. This pipeline has been tested with snakemake v7.32.4. Raw long-read sequencing files and the input contig genome assembly must be given in the config.yaml file. To execute the workflow run:
snakemake --use-conda --cores N
Or configure the cluster.json and run using the ./run_cluster command
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Version 2 (latest) Created 16th Mar 2024 at 07:45 by Tom Brown
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Version 1 (earliest) Created 16th Jun 2023 at 14:56 by Tom Brown
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Created: 16th Jun 2023 at 14:56
Last updated: 16th Mar 2024 at 07:49
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https://orcid.org/0000-0001-8293-4816
Welcome to the ERGA Space!
Here we collect, curate and develop pipelines to assemble and annotation reference-quality genomes for all eukaryotic life.
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Biodiversity Genomics Europe, funded by Horizon Europe call HORIZON-CL6-2021-BIODIV-01-01, aims at aligning the resources and research agendas of both DNA barcoding and reference genome generation, thus opening the door for a true quantum leap in biodiversity genomics research in Europe.
Despite ground-breaking developments in both DNA barcoding and full genome sequencing, there remains a critical need to develop and strengthen functioning communities of practice ...
Teams: Vertebrate Genomes Pipelines in Galaxy, Biodiversity Genomics Europe (general)
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Start date: 1st Sep 2022
End date: 28th Feb 2026
A collection of workflows and pipelines developed as part of the ERGA consortium
Space: ERGA
Public web page: https://www.erga-biodiversity.eu/
Collection of workflows designed to assembled a set of PacBio HiFi and Illumina HiC reads into a chromosome-scale de-novo assembly.
Development versions of these pipelines can be found in the ERGA github and any questions or queries can be raised on the ERGA Discussions Channel
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