RCAcorrect

The starting point for this pipeline is fastqs containing basecalled ONT reads. It is assumed that the genotype of the sample has already been determined and a concatenated (two-copy) reference sequence has been created for that genotype as well as a single-copy reference sequence.

First, run select_full_reads.sh
This looks for fastqs in $RUN_ID_PATH/fastq/pass, concatenates them into a single fastq and then trims adapters using porechop. Trimmed reads are then mapped with bwa-mem, and pysam is used to select reads with full-length mappings (of 3.2kb or more). The 3.2kb threshold can be changed by modifying the value of 'hbv_length' in select_full_reads.py

Inputs are:
./select_full_reads.sh $RUN_ID_PATH $OUTPUT_DIRECTORY $REFERENCE_FASTA $SAMPLE_ID

where the reference sequence should be two concatenated copies of the relevant genotype reference sequence.

Then, run chop_and_correct_RCA.sh
The steps carried out in this script are as follows:

(1) Select 100bp anchor at start of reference genome
(2) For each full length read: Find this anchor within the read using blast
(3) Chop up read based on anchor locations -> create fastq for this read
(4) Align these reads to (single) reference genome
(5) Correct sequences and write corrected consensus to fasta file
(6) Filter corrected reads to remove those with dual stand mappings or excessive gaps \

Inputs are:
./chop_and_correct_RCA.sh $OUTPUT_DIRECTORY $REFERENCE_FASTA $SAMPLE_ID $CORRECTION_TYPE

The output directory and sample ID should be the same as that given to select_full_reads.sh. The reference should in this case be a single copy genotype reference. Correction type should be one of consensus_only or error_correct.

Paths to relevant software are found near the top of each bash script and need to be appropriately modified before use. The scripts also use two python virtualenvs, $PORECHOP_VENV, in which porechop 0.2.3 is installed, and $PYSAM_VENV, the requirements for which can be found in pysam_venv_requirements.txt.