Table 1.
Summary of the CAFTOOLS
| A. General CAF utilities, including tools for communication with other software | |
| general CAF utilities | |
| cafpad | Converts an unpadded assembly to a padded one. All coordinate-dependent data are updated (written in C). |
| cafdepad | Inverse ofcafpad (C). |
| cafcat | Concatenates and consolidates multiple CAF files into a single file. Also reports semantic errors (C). |
| cafmerge | Merges two CAF files, replacing duplicated objects rather than concatenating them (cf.cafcat) (C). |
| caf2phrap | Extracts a subset of sequences from a CAF file into three files; (1) FASTA DNA; (2) base quality; (3) CAF stub of remaining attributes. This is used to prepare data forphrap but also provides a general way to extract FASTA sequence data from CAF (C). |
| assembler support | |
| cafphrap | Takes a CAF file and an optional list of reads, assembles them with phrap and creates a new CAF file describing the assembly. No other postprocessing is done. |
| caffak | Similar Perl wrapper forFAKII. |
| acembly support | |
| caf2bly | Converts a CAF file into an acemblydatabase. |
| bly2caf | Exports a CAF file from an acemblydatabase. |
| cafbly | Takes a CAF file and a script command file, reads a CAF file into an acembly database, performs the script, re-exports a CAF file on standard output and cleans up. |
| gap support | |
| caf2gap | Converts a CAF file into a gap4 database. All CAF tags are converted to their gap4 equivalents (C). |
| gap2caf | Creates a CAF representation of data in a gap4 database (C). |
| exp2caf | Converts Staden Experiment files into CAF. |
| updatecaf | |
| consed support | |
| consed2caf | Converts a phrap assembly or aconsed database into CAF. |
| consed2gap | Converts aphrap assembly or consed database into agap4 database. |
| caf2phd | Converts CAF reads tophred PHD files required forconsed. |
| phd2caf | Converts phred PHD files to CAf. |
| B. Specialized processing tools. Programs are written in Perl unless indicated otherwise. | |
| tag generators | |
| cafvector caftagfeature cafalu cafcgi | These wrappers extract contig sequence from CAF, screen it usingblast or crossmatch against a library of sequences, and create tags for any matches found. |
| auto-editor | |
| npedit | Proposes edits for an assembly by examining the SCF traces in the context of the alignment. A new CAF file is generated listing the suggested edits as special edit tags that are parsed and acted on byndedit (C). |
| ndedit | Makes the edits proposed by npedit. Editing will change the DNA sequences of the reads. ndedit modifies the coordinates of all tags and base qualities appropriately (C). |
| clipping | |
| ndclip | Clips back all assembled reads according to the Clipping tags. We use this to postprocess phrap assemblies to restrict aligned reads to their higher-quality regions (C). |
| neclip | Used after ndclip to extend back clipped reads where necessary to cover holes created (C). |
| cafsplit | Alternative to neclip. Splits contigs at holes. |
| finishing | |
| finish | Analyzes the assembly to choose directed reads for the purpose of finishing. |
| cafcop | Checks assembly for finishing errors and regions of insufficient sequence coverage. |
| clone overlap data management | |
| Readraid | Incorporates SCF traces and sequence of reads from overlapping regions of neighboring clones in the physical map. |
| Conraid | Incorporates consensus sequence from overlapping regions of neighboring clones. |
