Data processing and data analysis used for Hackflex performance testing

Manuscript: Hackflex: low cost Illumina sequencing library construction for high sample counts

Scripts for data processing, to be run in order:

001_library_processing.sh

filtering and trimming reads; reducing sizes of libraries to obtain equal size libraries

002_library_mapping.sh

mapping of reads against reference genome; removal of PCR duplicates; fragment size obtainment

003_library_alfred.sh

obtainment of quality stats (GC bias, coverage, read length, etc)

Scripts for the data analysis: (needs updating)

R version info: (needs updating)

platform: x86_64-apple-darwin15.6.0

status:

major: 3

minor: 6.1

year: 2019

month: 07

day: 05

svn rev: 76782

language: R

version.string: R version 3.6.1 (2019-07-05)

nickname: Action of the Toes

List of packages: (needs updating)

readr , readxl , data.table , tibble (v2.1.3) , openxlsx , splitstackshape , tidyr , tidyverse , dplyr , plyr (v1.$