Type: Nextflow
Creators: Usman Rashid, Chen Wu, Jason Shiller, Ken Smith, Ross Crowhurst, Marcus Davy, Ting-Hsuan Chen, Susan Thomson, Cecilia Deng
Submitter: Usman Rashid
Analysis of Chromosome Conformation Capture data (Hi-C)
The workflow takes trimmed HiC forward and reverse reads, and Hap1/Hap2 assemblies to produce Hap1 and Hap2 scaffolded assemblies using YaHS. It also runs all the QC analyses (gfastats, BUSCO, Merqury and Pretext).
The workflow takes a trimmed HiFi reads collection, Forward/Reverse HiC reads, and the max coverage depth (calculated from WF1) to run Hifiasm in HiC phasing mode. It produces both Pri/Alt and Hap1/Hap2 assemblies, and runs all the QC analysis (gfastats, BUSCO, and Merqury). The default Hifiasm purge level is Light (l1).
Tests This workflow take as input a collection of paired fastq. It uses HiCUP to go from fastq to validPair file. The pairs are filtered for MAPQ and sorted by cooler to generate a tabix dataset. Cooler is used to generate a balanced cool file to the desired resolution.
Flashlite-Juicer is a PBS implementation of Juicer for University of Queensland's Flashlite HPC.
Infrastructure_deployment_metadata: FlashLite (QRISCloud)
Type: Shell Script
Creators: Tracy Chew, Rosemarie Sadsad, Nathaniel Butterworth
Submitter: Tracy Chew
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Collection of de-novo genome assembly workflows written for implementation in Galaxy
Input data should be Oxford Nanopore raw reads plus Illumina WGS reads and Illumina 3-dimensional Chromatin Confirmation Capture (HiC) reads
Executing all workflows will output one scaffolded collapsed assembly and the complete QC analyses
Please run the workflows in order: WF0 (there are two, one for ONT, and another one for Illumina that can be used independently for the WGS and HiC reads), WF1, WF2, WF3, WF4
Maintainers: Diego De Panis
Number of items: 6
Tags: Assembly, Bioinformatics, Galaxy, Genomics, Genome assembly, ONT, illumina, Hi-C
Collection of de-novo genome assembly workflows written for implementation in Galaxy
Input data should be Oxford Nanopore raw reads plus Illumina WGS reads and Illumina 3-dimensional Chromatin Confirmation Capture (HiC) reads
Executing all workflows will output one scaffolded collapsed assembly and the complete QC analyses
Please run the workflows in order: WF0 (there are two, one for ONT, and another one for Illumina that can be used independently for the WGS and HiC reads), WF1, WF2, WF3, WF4
Maintainers: Diego De Panis
Number of items: 6
Tags: Assembly, Bioinformatics, Galaxy, Genomics, Genome assembly, ONT, illumina, Hi-C
Collection of de-novo genome assembly workflows written for implementation in Galaxy
Input data should be PacBio HiFi reads and Illumina 3-dimensional Chromatin Confirmation Capture (HiC) reads
Executing all workflows will output two scaffolded haplotype assemblies and the complete QC analyses
Please run the workflows in order: WF0 (there are two, one for HiFi and one for Illumina HiC), WF1, WF2, WF3, WF4
Maintainers: Tom Brown, Diego De Panis
Number of items: 6
Tags: Assembly, Bioinformatics, Galaxy, Genomics, Genome assembly, HiFi, Hi-C
