CSC

assemble... commands

assemble_independent
 -io             io_handle:integer
 -files          filenames:strings
?-output_mode    mode:integer(1)?
?-min_match      length:integer(20)?
?-min_overlap    length:integer(0)?
?-max_pads       count:integer(25)?
?-max_pmismatch  percentage:float(5.0)?
?-joins          to_join:integer(1)?
?-enter_failures to_enter:integer(0)?
?-tag_types      types:strings()?

assemble_new_contigs
 -io             io_handle:integer
 -files          filenames:strings

assemble_one_contig
 -io             io_handle:integer
 -files          filenames:strings

assemble_screen
 -io             io_handle:integer
 -files          filenames:strings
?-output_mode    mode:integer(1)?
?-min_match      length:integer(20)?
?-min_overlap    length:integer(0)?
?-max_pads       count:integer(25)?
?-max_pmismatch  percentage:float(5.0)?
?-save_align     to_save:integer(0)?
?-win_size       length:integer(0)?
?-max_dashes     count:integer(0)?
?-tag_types      types:strings()?

assemble_shotgun
 -io             io_handle:integer
 -files          filenames:strings
?-output_mode    mode:integer(1)?
?-min_match      length:integer(20)?
?-min_overlap    length:integer(0)?
?-max_pads       count:integer(25)?
?-max_pmismatch  percentage:float(5.0)?
?-joins          to_join:integer(1)?
?-enter_failures to_enter:integer(0)?
?-tag_types      types:strings()?

assemble_single_strand
 -io             io_handle:integer
 -files          filenames:strings
?-output_mode    mode:integer(1)?
?-min_match      length:integer(20)?
?-min_overlap    length:integer(0)?
?-max_pads       count:integer(25)?
?-max_pmismatch  percentage:float(5.0)?
?-joins          to_join:integer(1)?
?-enter_failures to_enter:integer(0)?

The assembly functions listed above all take similar arguments, but perform varying modes of assembly. The complete list of available arguments is listed below, but note that not all arguments apply to each function. Most functions return the failed readings and error codes with newlines between each reading and error code pair. Screen_only may return (when save_align is enabled) the reading alignment scores in a similar fashion.

-io io_handle

The database IO handle returned from a previous open_db call.

-files filenames

Filenames must contain a Tcl list of files to assemble.

-output_mode mode

Specifies the level of verbosity of the output. The default is 0. Mode must be one of the following.

1

Display no alignments

2

Display only passed alignments

3

Display all alignments

4

Display only failed alignments

-min_match length

Specifies the minimum length of exact match used during the hashing stage of assembly. The minium allowed value for this is 8. The default is 20.

-min_overlap length

This specifies the minimum length of an overlap between a reading and a consensus sequence. The default is 0 which implies no overlap is too short. Note that -min_match is still used so all overlaps have to be larger than that parameter in order to be found.

-max_pads count

After alignments the number of pads required in each of the two sequences (consensus and reading, or two consensuses) must be less than or equal to count. The default is 25.

-max_pmismatch percentage

After alignments the percentage of bases that do not match must be less than or equal to percentage. This is a floating point value. The default is 5.0.

-save_align to_save

This controls whether alignments scores are to be returned as the function result. A non zero value returns the scores. The default is 0.

-win_size length

-max_dashes count

During a screen-only assembly the cutoff data may be searched for matches. The criteria for determining how much cutoff sequence to align is selected as the portion where no more than count unknown ("-") bases within a region of length bases. Setting both these parameters to 0 means that cutoff data will be not searched. These are the defaults.

-joins to_join

This controls whether joins between contigs should be allowed. A non zero value allows joins. The default is 1.

-enter_failures to_enter

This controls whether failed readings should still be entered into the databases as single reading contigs. A non zero value will enable this. The default is 0.

-tag_types types

The assembly algorithm can mask segments of sequence covered by tags so that they are not used during hashing step and hence do not initiate overlaps. If types is a non blank list of tag types then masking will be applied to hide sequence covered by tags of these types from the initial hashing stage of assembly. The default is a blank list, which means no masking will be performed.