Bowtie2

# specified parameters

--n-ceil L,0,0.03
L: linear
the maximum number of ambiguous characters allowed in a read as a function of read length; specifying -L,0,0.03 sets the N-ceiling function f to f(x) = 0 + 0.03* x, where x is the read length.

--score-min C,-14,0
C: constant
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) = -14 + 0 * 1, where x is the read length.

--phred33
Input qualities are ASCII chars equal to the Phred quality plus 33. This is also called the "Phred+33" encoding, which is used by the very latest Illumina pipelines.

-X 50000
The maximum fragment length for valid paired-end alignments. E.g. if -X 100 is specified and a paired-end alignment consists of two 20-bp alignments in the proper orientation with a 60-bp gap between them, that alignment is considered valid (as long as -I is also satisfied). A 61-bp gap would not be valid in that case. If trimming options -3 or -5 are also used, the -X constraint is applied with respect to the untrimmed mates, not the trimmed mates.

-N 1
Sets the number of mismatches to allowed in a seed alignment during multiseed alignment. Can be set to 0 or 1. Setting this higher makes alignment slower (often much slower) but increases sensitivity. Default: 0.

-q/--quietbowtie2-build is verbose by default. With this option bowtie2-build will print only error messages.

# default parameters

--ma <int>
Sets the match bonus. In --local mode <int> is added to the alignment score for each position where a read character aligns to a reference character and the characters match. Not used in --end-to-end mode. Default: 2.