training_g4

This repository contains scripts and protocols for Docker/Garroway Labs at the University of Manitoba as they trainees go from raw fastq files through to VCF

Name		Name	Last commit message	Last commit date
Latest commit History 31 Commits
README.md		README.md
adapters.fa		adapters.fa
bcf_concat.sh		bcf_concat.sh
bcf_concat_NC_046070.sh		bcf_concat_NC_046070.sh
bcf_filter.sh		bcf_filter.sh
bgzip.sh		bgzip.sh
bgzip_long.sh		bgzip_long.sh
bowtie2_8threads.sh		bowtie2_8threads.sh
bowtie2_makeindex.sh		bowtie2_makeindex.sh
colin_vcftools_commands		colin_vcftools_commands
copy_stuff.sh		copy_stuff.sh
fastqc_mem_long.sh		fastqc_mem_long.sh
lamprey_colin_zoom.R		lamprey_colin_zoom.R
parsing_over_rep.R		parsing_over_rep.R
picard_remove_dups_3inputs.sh		picard_remove_dups_3inputs.sh
platypus_all.sh		platypus_all.sh
platypus_all_region_12hour.sh		platypus_all_region_12hour.sh
platypus_all_region_2day.sh		platypus_all_region_2day.sh
platypus_all_region_3hour.sh		platypus_all_region_3hour.sh
samtools_index.sh		samtools_index.sh
scaffold_progress_maker.R		scaffold_progress_maker.R
trimmomatic.sh		trimmomatic.sh