If I am working on Sanger sequencing results for a certain type of viruses, by assays that target parts of the genome, so I am using few assays for each sample, got a couple of sequencing reads for each sample. Then, assembly, MSA, then phylogenetics: Please, is there any recommended minimum sequence length (seq, bases number) for each read to consider it successful?, for example if after trimming of the low quality ends, I got read with 35 bp length?? can I consider it a successful sequencing? and can I use that read in MSA etc? of note, the other reads are of hundreds length.
Typical good Sanger reads will have between 600-900bp. Of course, sequencing length shouldn't be longer than whatever template you are sequencing. There are some features of the template that can interfere with sequencing, making reads shorter than they should - for example, long poly-A or poly-T (probably poly-C and poly-G as well), or if your template has length polymorphism.