Page Comparison

Raw reads

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• summarized denovo assemblies: 98 (46,971,194 contigs), 96 (27,839,279 contigs), 92 (18,493,729 contigs). Um, that’s a lot. Previously they aligned to the Helianthus annuus genome (v1.0). This was in Testing for evolutionary change in restoration: A genomic comparison between ex situ, native, and commercial seed sources of Helianthus maximiliani. We will use the v2.0 annuus genome (v2.0). It is in /project/evolgen/data/public/genomes/helianthus/GCF_002127325.2_HanXRQr2.0-SUNRISE_genomic.fna.gzNext up, use bwa to map against reference genome.

Assembly

10 Sep 2022 Working in /project/microbiome/data/seq/HMAX1/assem and assembling all reads in /project/microbiome/data/seq/HMAX1/demultiplex/sample_fastq/ against /project/evolgen/data/public/genomes/helianthus/GCF_002127325.2_HanXRQr2.0-SUNRISE_genomic.fna.gz.

1. Ran bwa index -a bwtsw GCF_002127325.2_HanXRQr2.0-SUNRISE_genomic.fna.gz by hand in an interactive node

2. Commands are in 0_assem.nf. Run this with nextflow run -bg 0_assem.nf -c teton.config. These are jobs are using: module load swset/2018.05 gcc/7.3.0 bwa/0.7.17 samtools/1.12 as specified in teton.config in this directory (bwa is version 0.7.17-r1188). Output is in /project/microbiome/data/seq/HMAX1/assem/sambam/. Gave each job 60 minutes, which was unnecessarily long, but conservative. Longest running jobs I could see were less than 20 minutes. Moved all 477 inputs files through in about 30 minutes total.

Variant calling

… working here …

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Copying steps from https://github.com/zgompert/DimensionsExperiment

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