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Home Page: https://akikuno.github.io/cstag/cstag
License: MIT License
Python module to manipulate and visualize minimap2's cs tag
Home Page: https://akikuno.github.io/cstag/cstag
License: MIT License
複数のcstagのconsensusを作る関数
import cstag
cs_list = ["cs:Z:=ACGT", "cs:Z:=AC*gt*T", "cs:Z:=AC*gt*T"]
cstag.consensus(cs_list)
# cs:Z:=AC*gt*T
Output a html report from cs tag
For the JoSS review at openjournals/joss-reviews/issues/6066.
The CS
(uppercase) is a reserved for color read sequence information as per the SAM format, while the cs
(lowercase)
tag represents the difference string. This has already been a topic of discussion while feature requests to incorporate the cs
tag more
formally into the SAM format.
It might be beneficial to change the "CS" to "cs" in all documentation so as to not mislead users.
Not sure if this is feasible to implement, but I wanted to make this request which would make cstag
more useful to our group.
Right now the consensus
function doesn't contain any mechanism for checking the "quality" of the consensus. In our work, we often want to try to call a consensus, but also be able to discard sets of reads if the consensus isn't in good agreement. This is common in sequencing of amplicons for many purposes. Eg, we would ideally like:
samファイルからcstagを呼び出す関数 calcsの移植
cs tagをMIDSに変換する関数
Mask nucleotide with low phred score into N
.
For the JoSS review at openjournals/joss-reviews/issues/6066
Please see https://github.com/betteridiot/joss_reviews/blob/master/cstag/joss_review.md for complete notes.
Doctests for cstag
do not pass due to minor syntax errors. See Testing doctests. As doctests should also be testable (given their nature), this should be addressed.
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