A LAMP concatemer (lamplicon) polisher to improve single read accuracy.

First, install samtools-1.10, bcftools, and minimap2.

Next, install lamprey:

$ git clone https://github.com/jackwadden/lamprey
$ cd lamprey
$ python3.7 -m venv venv3 --prompt lamprey
$ source venv3/bin/activate
(lamprey) $ pip install --upgrade pip
(lamprey) $ pip install -r requirements.txt

The following will convert all lamplicon sequences to files of separated concatemer sequences.

$ python3 lamprey.py primer_set.primers lamplicons.fastq

The following will align each separate mer into out.sam.

$ minimap2 -a \
     -x map-ont \
     --eqx \
     -t 1 \
     -w 1 \
     -o mers.sam \
     ref.fa \
     mers.fa

The following will convert the aligned mers to a sorted BAM file.

$ scripts/sam_to_bam.sh mers.sam

The following will generate a consensus sequence (out_cns.fa) from the aligned mers.

$ scripts/generate_consensus.sh ref.fa out.bam

The following will align the consensus sequence to a reference.

$ minimap2 -a \
     -x map-ont \
     --eqx \
     -t 1 \
     -w 1 \
     -o mers_cns.sam \
     ref.fa \
     mers_cns.fa

The following will compute the average error of the original aligned mers and the polished concensus sequence.

$ python3 scripts/error_rate.py mers.sam
$ python3 scripts/error_rate.py mers_cns.sam

F3 ATGTCGTGCCGTTG
F2 ATGCGTATAGATGTATAGA
F1c AAAATTTTGGGGCCCC
FLP ATGTTTGGTTGAGATG
T ATATATATATATATAAT