| gap4 | Performs assembly, contig joining,
assembly checking, repeat searching, experiment suggestion,
read pair analysis and contig editing. Has graphical views of
contigs, templates, readings and traces which all scroll in register.
Contig editor searches
and experiment suggestion routines use phred confidence values
to calculate the confidence of the consensus sequence and hence
only identify places requiring visual trace inspection or extra data.
The result is extremely rapid finishing and a consensus of known
accuracy. |
| gap5 | This is the new development version of Gap4, designed to
work with the large volumes of data attainable through the
newer sequencing technologies (eg Illumina, SOLiD, 454).
At present documentation is absent, but it shares many common
features with Gap4. |
| tg_index | Generates Gap5 format databases from input assembly
formats: SAM, BAM, MAQ, ACE, etc. |
| tg_view | A text-mode viewer for Gap5 databases. |
| pregap4 | Provides a graphical user interface to set up the processing
required to prepare trace data for assembly or analysis; and also
gives a method for its automation. The possible processes which
can be set up include trace format conversion, quality analysis,
vector clipping, contaminant screening and repeat searching. |
| qclip | Performs simple quality clipping of Experiment Files based
on confidence values or on the sequence composition. |
| polyA_clip | Marks polyA and polyT heads and tails. |
| stops | Identifies Sanger sequencing "stops" in SCF and ZTR trace files. |
| vector_clip | Finds and marks (with tags) vector segments of sequence readings
stored as Experiment Files. Rapid and sensitive, and usually
used via pregap4. |
| screen_seq | Searches sequence readings stored as Experiment Files
for matches against sets of possible contaminant
sequences. Typically used to look for E.Coli or yeast
contamination. Very fast, and usually used via pregap4. |
| find_renz | Finds and marks (with tags) known repeat sequences ( e.g. ALUs)
in sequence readings stored as Experiment Files.
Usually used via pregap4. |
| trev | A rapid and flexible viewer and editor for
ABI, ALF or SCF trace files. Provides good
support for interaction with Experiment Files. |
| tracediff | Automatically locates point mutations by comparing new traces against those of a reference trace. Handles any number of files in a single run and prepares results which can be viewed in gap4. |
| mutscan | Used in conjunction with tracediff to search for heterozygous positions and, where they coincide, to label tracediff results appropriately. |
| gap4 | For viewing aligned sequences and traces and checking automatic
mutation assignments. Can subtract traces and display their
differences. |
| spin | A combination of the older nip4 and sip4 program. Spin compares
pairs of sequences in many ways, often presenting
its results graphically. Has very rapid dot matrix analysis,
global and local alignment, plus a sliding sequence window linked to
the graphical plots. Can compare nucleic acid against nucleic acid,
protein against protein, and protein against nucleic acid.
Analyses nucleotide sequences to find genes, restriction sites,
motifs, etc. Performs translations, finds open reading frames, counts
codons, etc. |
| make_weights | Analyses a multiple alignment to produce a weight matrix for use
within spin. |
| create_emboss_files | Creates the GUI interface files for Spin from emboss ACD
files. Only needs to be run once after a new EMBOSS release. |
| convert_trace | Converts traces from any format to any format. Also handles
trace background subtraction and normalisation. |
| get_comment | Extracts text from the comment fields from any trace
format. Replaces the get_scf_field program. |
| index_tar | Produces a text index from a tar file. Used for speeding up
RAWDATA access within gap4. |
| getABIstring | Displays arbitrary string fields from an ABI trace file. |
| getABIhex | Displays arbitrary fields from an ABI trace file as hex codes. |
| getABIraw | Displays arbitrary fields from an ABI trace file in the raw
format. |
| getABIcomment | Displays the comments from an ABI trace file. Equivalent to
getABIstring CMNT. |
| getABISampleName | Displays the sample name (reading name) stored in an ABI trace
file. Equivalent to getABIstring SMPL |
| getABIdate | Displays the run date from an ABI trace file. |
| alfsplit | Splits the Pharmacia ALF gel file into multiple files. This is
necessary before processing by pregap4. |
| makeSCF | Converts existing trace files (whatever format) into SCF
files. |
| scf_info | Displays details stored in the header of an SCF file. |
| scf_dump | Displays the entire SCF file contents in a human readable
format. |
| scf_update | Converts between SCF file versions (2 to 3 and vice versa). |
| get_scf_field | Extracts data from the SCF comment section. |
| eba | Estimates the base accuracy of each base in an SCF file. |
| convert | Converts between the various assembly database formats. |
| copy_db | Copies and garbage collects gap4 databases. |
| copy_reads | Aligns two gap4 databases and copies overlapping
sequences from one to the other. |
| extract_seq | Extracts the sequence component from trace files or
experiment files. |
| init_exp | Extracts the sequence and related information from trace files to output in Experiment File format. |
| stash | General purpose scripting interface to Gap4 and Spin,
be used for producing graphical scripts and interfaces. |
| splitseq_da | Splits large sequences into a set of overlapping smaller
sequences. Outputs the sequences in a Experiment File format
with attributes suitable for input using Directed Assembly. |