Ampseer examines reads in fastq format and identifies which multiplex PCR primer set was used to generate the SARS-CoV-2 sequencing library they are read from. It is intended to differentiate between ARTIC v3, ARTIC v4, ARTIC v4.1, VarSkip 1a, VarSkip 2, Midnight and VarSkip Long primer sets sequenced by Illumina or ONT.
nextera transposases cannot insert at the extreme ends of amplicons. To handle these libraries, it would be necessary to enable partial matches with expected start sequences.
bwlang
commented
2 years ago 
nextera transposases cannot insert at the extreme ends of amplicons. To handle these libraries, it would be necessary to enable partial matches with expected start sequences.