diff --git a/readme.md b/readme.md index 4d4f616..950cf4a 100644 --- a/readme.md +++ b/readme.md @@ -204,6 +204,7 @@ Options for creating a Graph/Data file: * The read depth (number of times each sequence is read) * The read error rate (probability a sequence is misread) * The error collision rate (probability two misreads produce the same spurious sequence) + * The real sequence collision rate (probability that a misread will produce a different, real sequence from the sample plate. Only applies to new misreads; once an error of this type has occurred, it's likelihood of ocurring again is dominated by the error collision probability.) These files do not have a human-readable structure, and are not portable to other programs. @@ -361,6 +362,7 @@ roughly as though it had a constant well population equal to the plate's average * ~~Add read depth simulation options to CLI~~ DONE * ~~Update graphml output to reflect current Vertex class attributes~~ DONE * Individual well data from the SequenceRecords could be included, if there's ever a reason for it +* ~~Implement simulation of sequences being misread as other real sequence~~ DONE * Update matching metadata output options in CLI * Update performance data in this readme * Re-implement CDR1 matching method