Bowtie 2: Manual

Scoring options

--mp MX,MN
Sets the maximum (MX) and minimum (MN) mismatch penalties, both integers. A number less than or equal to MX and greater than or equal to MN is subtracted from the alignment score for each position where a read character aligns to a reference character, the characters do not match, and neither is an N. If --ignore-quals is specified, the number subtracted quals MX. Otherwise, the number subtracted is MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) ) where Q is the Phred quality value. Default: MX = 6, MN = 2.

Sets penalty for positions where the read, reference, or both, contain an ambiguous character such as N. Default: 1.

--rdg ,
Sets the read gap open () and extend () penalties. A read gap of length N gets a penalty of + N * . Default: 5, 3.

--rfg ,
Sets the reference gap open () and extend () penalties. A reference gap of length N gets a penalty of + N * . Default: 5, 3.

Sets a function governing the minimum alignment score needed for an alignment to be considered "valid" (i.e. good enough to report). This is a function of read length. For instance, specifying L,0,-0.6 sets the minimum-score function f to f(x) = 0 + -0.6 * x, where x is the read length. See also: setting function options. The default in --end-to-end mode is L,-0.6,-0.6 and the default in --local mode is G,20,8.

--mp: ミスマッチペナルティ(最大,最小)、リードのクオリティでスコアがバラける。
--np: N(曖昧塩基)のペナルティ、Bowtie2では他の縮退塩基もNとして扱われる。
--rdg: リードのギャップペナルティ(開始,延長それぞれについて規定)
--rfg: 参照配列のギャップペナルティ(開始,延長それぞれについて規定)

であり、これは以下のように書いてあるが、要約するとリードの長さを変数としたときの "式のタイプ, y切片,傾き" である。

Setting function options

Some Bowtie 2 options specify a function rather than an individual number or setting. In these cases the user specifies three parameters: (a) a function type F, (b) a constant term B, and (c) a coefficient A. The available function types are constant (C), linear (L), square-root (S), and natural log (G). The parameters are specified as F,B,A - that is, the function type, the constant term, and the coefficient are separated by commas with no whitespace. The constant term and coefficient may be negative and/or floating-point numbers.

For example, if the function specification is L,-0.4,-0.6, then the function defined is:

f(x) = -0.4 + -0.6 * x
If the function specification is G,1,5.4, then the function defined is:

f(x) = 1.0 + 5.4 * ln(x)
See the documentation for the option in question to learn what the parameter x is for. For example, in the case if the --score-min option, the function f(x) sets the minimum alignment score necessary for an alignment to be considered valid, and x is the read length.


--mp "1,1" --rdg "0,1" --rfg "0,1" --score-min "C,-1,0"

”C”については例示すら無いが一応これでちゃんと動くのは確認した。(SAMファイル内で "XM:i:" が1を超えるものがなかった。)