-d, or

--disable-all-filters

off

When on, disables all filtering and trimming and overrides other filtering and trimming settings.

-k, or

--keypass-filter

on

When on, filters out reads that do not both produce a signal and match the library key (or the test fragment key).

--min-read-length

25

(Int)

F ilters out reads less than this minimum read length.

This filter screens out poor reads early on to avoid wasting processing time on them. See also --trim-min-read-len, which sets the minimum length threshold that is applied after trimming.

--prefix-mol-tag

Empty

Base structure of 5’ unique molecular tag (ACGTN bases) to be trimmed after the barcode adapter.

--suffix-mol-tag

Empty

Base structure of 5’ unique molecular tag (ACGTN bases) to be trimmed before P1 adapter.

--extra-trim-left

0

(Int)

Trims this number of bases beyond the barcode adapter and the 5' unique molecular tag (if applicable).

--extra-trim-right

0

Trims this number of bases at the 3' end of the template before the 3' unique molecular tag (if applicable) and the P1 adapter. Only done if P1 adapter was found.

--trim-adapter-cutoff

16

( Float)

A score cutoff value.

Smaller values correspond to more stringent adapter search and larger values to less stringent adapter search.

Set to 0 to turn off.

--trim-adapter-min-match

6

(Int)

The minimum number of P1 adapter bases required in order to trim the P1 adapter.

--trim-qual-window-size

30

( Int)

Window size for quality trimming.

--trim-qual-cutoff

16

( Float)

Cutoff for quality trimming.

Set to 100 to turn off. When set to 100, no reads are filtered out due to this parameter.

--trim-min-read-len

25

(Int)

Filters out any readsthat fall below this minimum read length after anytrimming step. By default it is initialized with the value of 'min-read-length'.