WORKFLOW: Hybrid Assembly
The Hybrid Assembly workflow is used for generating hybrid Nanopore+Illumina assemblies in parallel for multiple samples. It will produce two assemblies per sample by default, one where Illumina sequencing data is subsampled and one using the full Illumina sequencing dataset.
| Parameter Identifier | Parameter Value Type / Default | Parameter Description |
|---|---|---|
| read_subsampling | Integer. 2500000 | The number of Illumina reads to subsample for the construction of the assembly where it is performed. Should correspond to 100X coverage. |
| nanomerge_memory | Integer. 24 | The memory (in Gb) to use for merging Nanopore FASTQs. |
| nanomerge_timelimit | String. 02:00:00 | The time limit for merging Nanopore FASTQs. |
| nanotrim_memory | Integer. 24 | The memory (in Gb) to use for Porechop to trim adapters from Nanopore FASTQ. |
| nanotrim_timelimit | String. 10:00:00 | The time limit for trimming Nanopore FASTQ. |
| fastqfilter_options | String. -l 3000 -L 20000 -b 300000000 | Options for subsampling of Nanopore FASTQ using fastqfilter script in /path/to/seQuoia/scripts/
|
| nanosubsample_memory | Integer. 32 | The memory (in Gb) to use for fastqfilter subsampling of Nanopore FASTQ. |
| nanosubsample_timelimit | String. 10:00:00 | The time limit for subsampling of Nanopore FASTQ. |
| unicycler_options | String. --mode normal --verbosity 2 | Options for running Unicycler hybrid assembly. |
| unicycler_threads | Integer. 4 | The number of cores/threads to use for running Unicycler. |
| unicycler_memory | Integer. 16 | The memory (in Gb per core/thread) to use for running Unicycler. |
| unicycler_timelimit | String. 48:00:00 | The time limit for running Unicycler. |
| pilonpolishing_max_iterations | Integer. 10 | The max number of iterations to perform when performing iterative assembly refinement using Pilon. |
| pilonpolishing_threads | Integer. 4 | The number of cores/threads to provide Pilon for iterative refinement. |
| pilonpolishing_memory | Integer. 8 | The memory (in Gb per core/thread) to use for running Pilon for iterative refinement. |
| pilonpolishing_timelimit | String. 24:00:00 | The time limit for running Pilon based iterative assembly refinement. |
| run_guinan | Boolean. False | Whether to run GAEMR/Guinan suite for secondary sanity check of adapters making it into the assembly. Currently only works on Broad servers. |
| contig_size_filter | Integer. 0 | Whether to filter contigs shorter than a certain length. |
| run_gaemr_ont | Boolean. False | Whether to run GAEMR with Nanopore read coverage accounted for. Currently only works on Broad servers. |
| gaemr_formatter_options | -g 1 -c 100 -r | Options to use for GAEMR assembly formatting/preparation for QC analysis. |
| gaemr_qc_options | _--force --analyze_rna | Options to use for running GAEMR assembly QC analysis. |
| gaemr_threads | 2 | The number of cores/threads to provide GAEMR for iterative refinement. |
| gaemr_memory | 32 | The memory (in Gb per core/thread) to use for running GAEMR. |
| gaemr_timelimit | String. 24:00:00 | The time limit for running GAEMR assembly QC. |
| run_canu | Boolean. False | Whether to create a third assembly using only Nanopore data with canu. |
| canu_options | String. stopOnReadQuality=false genomeSize=5m | Options to run canu with. |
| canu_threads | Integer. 4 | The number of cores/threads to provide canu assembly. |
| canu_memory | Integer. 24 | The memory (in Gb per core/thread) to use for running canu. |
| canu_timelimit | String. 07:00:00:00 | The time limit for running canu assembly. |
| run_nanopolish | Boolean. False | Whether to perform nanopolish refinement of canu assembly. |
| nanopolish_options | String. | Options for nanopolish variants. |
| nanopolish_threads | Integer. 16 | The number of cores/threads to provide nanopolish. |
| nanopolish_memory | Integer. 10 | The number of memory (in Gb per core/thread) to use for nanopolish. |
| nanopolish_timelimit | String. 72:00:00 | The time limit for running nanopolish assembly refinement. |
| run_pilon_on_canu | Boolean. True | Whether to run pilon refinement on canu assembly. |
| run_reorganize | Boolean. True | Whether to restructure/organize the directory structure for each sample after all steps have run. |