From 4e174b7217bc3817ac8b9619c5261ccd7ff2d289 Mon Sep 17 00:00:00 2001 From: Zev Kronenberg Date: Tue, 27 Apr 2021 09:46:47 -0600 Subject: [PATCH] Update README.md --- README.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/README.md b/README.md index b95ded3..90dfa89 100644 --- a/README.md +++ b/README.md @@ -201,6 +201,11 @@ We've optimized the default parameters to perform well on several datasets. In g ### Provide an off-target-groups file. Amplification can generate off target reads. Similarly, pbaa can accidentally place a few reads in the wrong grouping/locus. These reads may generate clusters that are off-target (not amplified). By providing a list of guide-names / group-names (one per line), pbaa will filter these out. +### Understanding the error correction stage options +![HiFi Amplicon Analysis Workflow](img/error_correction.png) + +There are four hurestics to consider adjusting depending on the experiment (_max-reads-per-guide_, _max-alignments-per-read_, _pile-size_, _min-var-frequency_). In the above image, there are a total of _max-reads-per-guide_ to consider for each HiFi (A-read). An A-read is randomly aligned to _max-alignments-per-read_. These alignments are sorted in decreasing sequence idenity. A total of _pile-size_ reads are retained to correct the A-read. The _min-var-frequency_ is the fraction of reads within a _pile_ that support that the A-read is correct at any position along the A-read. + ## Advanced / Hidden Options