Repository for ngs scripts I use regularly.
- align_RAD_2019.sh = alignment of RAD data from R1 and R2 fastq files (markdup, fixmate)
- align_ind_fa_2019.sh = basic alignment of data from single fastq file
- barcodes_pst1.csv = comma separated list of Pst1 barcodes
- barcodes_sbf1.csv - comma separated list of Sbf1 barcodes
- BarcodeSplitList3Files.pl = perl script to split lanes based on given barcode
- BCsplitBestRadPE2.pl = perl script to split each lane by wells via inline barcode. NOTE right now requires barcodes to be given in line––make sure the barcodes match the RE
- BUSCOv?.sh = script to run BUSCO version x
- RUN_alignment_RAD.slurm = slurm script to submit for aligning RAD PE data
- splitRAD_Pst1.sh = shell script to split lanes and barcodes of RAD data prepped with RE=Pst1
- splitRAD_Sbf1.sh = shell script to split lanes and barcodes of RAD data prepped with RE=Sbf1