README file to give information about my scripts: Contact: [email protected] (external email)

picarding.sub --> script that tries to generate a dictionary genome file using the picard.jar software Note: picard path can be found only by using $PICARDPATH

Prefast.py --> python script (non-functional through the cluster/use it locally) to retreive the RNAseq data using prefetch (did it in my WUR thesis)

bam_statistics.sub --> bash script including multiple statistics using samtools: - samtools flagstat - samtools stats - samtools view - samtools checkquality

mummer_pipeline.sh --> runs mummer pipeline for seq alignnment: - samtools faidx - nucmer - mummerplot - show-diff - show-aligns

find_the_chimeric.sub --> bash script: uses the grep and awk functions to retreive the chimeric alignmens within the area of 37Mbp and 47Mbp of chromosome 2B(LSYQ02000004.1)

fill_the_Ns.sub --> bash script - tgsgapcall : to fill the NNNs of the Wild Emmer genome assembly using the long-read sequencing data I applied it using the TRI18485 southern Levant data against the WEW v2.0 genome

conda_script.sh --> download modules through the conda environment (my_env)

remove_dups.sub --> removes PCR duplicates from the sequencing data - picard tools Note: use the flagstats to check the PCR duplicates (generated: bam_statistics.sh

merge_fastqs.sub --> merges two fastq files, in order to be used in the tgsgapcloser script