This repository contains scripts used to process and manage output sequence data and metadata related to Illumina hiseq and miseq machines, including running a number of GBS-specific Q/C steps for predominately GBS-related sequencing output. This project is focused on immediate upstream Q/C and sequence delivery, rather than custom downstream analyses.

Refer to DECONVQC.docx for more details

This resource contributes to and is partly supported by the MBIE programme "Genomics for Production & Security in a Biological Economy"

Below is a summary of the contents of the repository

#Database ##Schema

• setup.psql
• setup_quick_reports.psql

#Keyfile and run data management

• deleteKeyfile.psql
• get_keyfilename.psql
• updateFastQLocationInKeyFile.psql
• checkKeyFiles.psql
• extractKeyfile5.psql
• extract_sample_species.psql
• extractKeyfile.psql
• get_fastq_link.psql
• addRun.sh
• get_enzyme_count_from_database.sh
• get_lane_from_database.sh
• is_keyfile_in_database.sh
• deleteKeyfile.sh
• get_enzyme_from_database.sh
• importKeyfile.sh
• is_run_in_database.sh
• updateFastqLocations.sh
• extractKeyfile.sh
• get_flowcellid_from_database.sh
• importOrUpdateKeyfile.sh
• listDBKeyfile.sh
• sanitiseKeyFile.py

#Generic Sequence Q/C (i.e. not GBS-specific) ##Fastqc ##Alignment of sample against references

• run_mapping_preview.sh

##Contamination check - alignment of random sample of reads against nt

• run_sample_contamination_checks.sh
• summarise_global_hiseq_taxonomy.sh
• summarise_global_hiseq_taxonomy.py
• taxonomy_clustering.r

##GBS Q/C

###Tassel

• link_key_files.sh
• summarise_global_hiseq_reads_tags_cv.sh
• summarise_read_and_tag_counts.py
• summarise_hiseq_taxonomy.py
• get_reads_tags_per_sample.py
• tags_plots.r

###KGD

• batch_kgd.sh
• run_kgd.sh
• GBS-Chip-Gmatrix.R
• run_kgd.R

###k-mer analysis

• kmer_entropy.py
• kmer_plots_gbs.r

#Overall workflow

• process_hiseq1.0.sh
• gbs_hiseq1.0.sh
• archive_hiseq1.0.sh
• process_hiseq1.0.mk
• gbs_hiseq1.0.mk
• archive_hiseq1.0.mk
• get_processing_parameters.py
• species_config.txt

#Presenting Results to Users

• extract_peacock.psql
• make_peacock_plots.sh
• make_peacock_plots.py
• make_run_plots.py

#Project Lifecycle

• clean_hiseq_run.sh
• fix_archived_run_fastq_links.sh

#Utilities

• cat_tag_count.sh
• tags_to_fasta.py
• prbdf.py

#Documentation

• DECONVQC.docx