tijeco/oyp

Oyster River Protocol workflow and scripts

OYP

Oyster River Protocol workflow and scripts (assuming paired end data)

Trim reads in trim_galore

trim_galore --paired {fastq1} {fastq2} -q 2

Correct reads with rcorrector

perl run_rcorrector.pl  -k 31 -t 30 -1 {trimmed_fastq1} -2 {trimmed_fastq2}

Assemble in Trinity

Trinity  --seqType fq --left {corrected_fastq1} --right {corrected_fastq2} --max_memory 100G --CPU 23 --output trinity_anahita --no_normalize_reads

*** Get coding sequences using transdecoder***

TransDecoder.LongOrfs -t Trinity.fasta  -m 30

Note: It is also advisable to blast the entire assembly against nr database and remove contaminant transcripts, scripts for this will follow