From 48734352bbfede5c60337c4723dcef3c00aedf13 Mon Sep 17 00:00:00 2001 From: jonas-fuchs Date: Tue, 17 Oct 2023 00:06:36 +0200 Subject: [PATCH] updated docs --- docs/how_varvamp_works.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/how_varvamp_works.md b/docs/how_varvamp_works.md index 52009ac..5d02297 100644 --- a/docs/how_varvamp_works.md +++ b/docs/how_varvamp_works.md @@ -23,7 +23,7 @@ varVAMP searches for potential primer regions as defined by a user-defined numbe varVAMP uses [`primer3-py`](https://pypi.org/project/primer3-py/) to search for potential primers. Some of the evaluation process, determining if primers match certain criteria, was adapted from [`primalscheme`](www.github.com/aresti/primalscheme). The primer search contains multiple steps: 1. Digest the primer regions into kmers with the min and max length of primers. This is performed on a consensus sequence that does not contain ambiguous characters but is just the majority consensus of the alignment. Therefore, primer parameters will be later calculated for the best fitting primer. 2. Evaluate if these kmers are potential primers independent of their orientation (temperature, GC, size, poly-x repeats and poly dinucleotide repeats) and dependent on their orientation (secondary structure, GC clamp, number of GCs in the last 5 bases of the 3' end and min 3' nucleotides without an ambiguous base). Filter for kmers that satisfy all constraints and calculate their penalties (explained in the last section). -3. Sanger and tiled mode: Find lowest scoring primer. varVAMP sorts the primers by their score and always takes the best scoring if the primer positions have not been covered by a better primer. This greatly reduces the complexity of the later amplicon search while only retaining the best scoring primer of a set of overlapping primers. +3. Sanger and tiled mode: Find lowest scoring primer. varVAMP sorts the primers by their score and always takes the best scoring if the left half of the primer has not been covered by a better primer. This greatly reduces the complexity of the later amplicon search while only retaining the best scoring primer of a set of overlapping primers. ### Amplicon search