README

This repository contains scripts used for genome analysis of ABC funded almond genome resequencing.

All scripts were run using the UC Davis CAES cluster (except as noted).

Scripts include:

• angsd.sh (not yet created)
• bwa.sh
• fastqc.sh
• merge.sh (not yet implemented)
• phase.sh
• popbam.sh (not yet implemented)
• sam.sh
• samstat.sh
• scythe.sh
• sickle.sh

bwa.sh

Arrayed read mapping using BWA-mem for multiple accessions declared in an array.

fastqc.sh

Quality control of fastq files using FastQC, a java program that produces zipped html output.

merge.sh

For merging BAM files to use with PopBAM.

phase.sh

Phasing BAM files with samtools for use in PopBAM.

popbam.sh

Getting population genetics data directly from BAM files using PopBAM.

sam.sh

Filler script to rename files from stdout to sam due to accidental oversight not directing stdout to file.

samstat.sh

Evaluate SAM and or BAM files. In this case original BWA-mem read mapping and samtools phased BAM files, including chimeric reads. (It can evaluate FASTA and FASTQ, but not if they are gzipped - produces segmentation fault - use FastQC.)

scythe.sh

Trim adapter sequence from FASTQ reads. (Need to include lines to gzip output files and remove non-gzipped output.)

sickle.sh

Trim low quality bases from adapter-trimmed FASTQ reads, gzip output files, and remove non-gzipped output.