WhitefishReferenceGenome

Scripts used for Coregonus sp. "Balchen" genome assembly/analysis in De-Kayne, Zoller & Feulner 2020

If you use/adapt any of these scripts please cite the associated paper: https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13187

For chromosome-scale scaffolds of wtdbg2 assembly see European Nucleotide Archive accession ERZ1303334 (formerly ERZ1030224) Unscaffolded contigs (7815) are included here as two files: AWG_v1.unscaffolded1.fastq.gz and AWG_v1.unscaffolded2.fastq.gz

Parameters/submission scripts are included for:

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Assembly using Falcon Canu and wtdbg2

• FalconAssembly.txt - parameters for Falcon assembly by DNA Nexus
• CanuAssembly.txt - parameters for Canu assembly
• wtdbg2Assembly.txt - parameters for wtdbg2 assembly

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Purge_haplotigs

• PurgeHaplotigs.txt - all commands for purging of haplotigs for each assembly
• submit.purge_haplotigs.sh - submission script for purge_haplotigs

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Analysis and validation of assemblies (estimation of genome size, assessing coverage of Illumina data and confirming synteny to linkage map)

• GenomeAssessmentAnalysis.txt - all commands run for estimation of genome size and analysis of each genome assembly

  • cov.per.window.pl - for coverage analysis

• PhaseSynteny_FR2_MOLECOLRES.R - R script for coverage and synteny analysis of Falcon assembly

  • FalconR2ChromosomeLenghts.txt - falcon assembly chromosome lengths
  • SA_linkagemap_FalconR2PhaseMapped_Filtered.csv - mapping of SA linkage map to Falcon assembly

• PhaseSynteny_CR2_MOLECOLRES.R - R script for coverage and synteny analysis of Canu assembly

  • CanuR2ChromosomeLenghts.txt - falcon assembly chromosome lengths
  • SA_linkagemap_CanuR2PhaseMapped_Filtered.csv - mapping of SA linkage map to Canu assembly

• PhaseSynteny_WR2_MOLECOLRES.R - R script for coverage and synteny analysis of wtdbg2 assembly

  • wtdbg2ChromosomeLenghts.txt - falcon assembly chromosome lengths
  • SA_linkagemap_Wtdbg2PhaseMapped_Filtered.csv - mapping of SA linkage map to wtdbg2 assembly

• LM_stats.txt

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Repeat masking

• RepeatAnnotationCommands.txt - all commands for repeat masking of each assembly
• SalmonidaeRepbase.lib - Salmonidae repeat library used in repeat annotation

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Annotation

• MakerCommands.txt - all commands for MAKER2 annotation of wtdbg2 assembly
  • prepare.gff-merge.command.sh
  • gff_merge.command.sh
  • collect.maker.fastas.sh

parameter files for round one of maker (remove _r1 to use):

• maker.run.cmd_r1.sh
• prep.and.start.maker.runs_r1.sh
• maker_bopts.ctl
• maker_exe.ctl
• maker_opts_r1.ctl

modified parameter files for round 2 and round 3 of maker (remove _r23 to use maker.run.cmd.sh and prep.and.start.maker.runs.sh in rounds 2 and 3 of annotation) (remove _r2 or _r3 to use maker_opts.ctl in rounds 2 and 3 of annotation):

• maker.run.cmd_r23.sh
• prep.and.start.maker.runs_r23.sh
• maker_opts_r2.ctl
• maker_opts_r3.ctl

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Symap/sequence similarity

• to.extract.lsf
• from.extract.lsf
• lastz_submitscript_extend2.lsf