Contig

A contig (from contiguous) is a set of overlapping DNA segments that together represent a consensus region of DNA. In bottom-up sequencing projects, a contig refers to overlapping sequence data (reads); in top-down sequencing projects, contig refers to the overlapping clones that form a physical map of the genome that is used to guide sequencing and assembly. Contigs can thus refer both to overlapping DNA sequence and to overlapping physical segments (fragments) contained in clones depending on the context.

Sequence contigs

A sequence contig is a contiguous, overlapping sequence read resulting from the reassembly of the small DNA fragments generated by bottom-up sequencing strategies. This meaning of contig is consistent with the original definition by Rodger Staden (1979). The bottom-up DNA sequencing strategy involves shearing genomic DNA into many small fragments ("bottom"), sequencing these fragments, reassembling them back into contigs and eventually the entire genome ("up"). Because current technology allows for the direct sequencing of only relatively short DNA fragments (300–1000 nucleotides), genomic DNA must be fragmented into small pieces prior to sequencing. In bottom-up sequencing projects, amplified DNA is sheared randomly into fragments appropriately sized for sequencing. The subsequent sequence reads, which are the data that contain the sequences of the small fragments, are put into a database. The assembly software then searches this database for pairs of overlapping reads. Assembling the reads from such a pair (including, of course, only one copy of the identical sequence) produces a longer contiguous read (contig) of sequenced DNA. By repeating this process many times, at first with the initial short pairs of reads but then using increasingly longer pairs that are the result of previous assembly, the DNA sequence of an entire chromosome can be determined.

Contig (defragmentation utility)

Contig is a command line defragmentation utility for Windows currently owned by Microsoft subsidiary SysInternals.

Operation

Contig is designed to defragment individual files, or specified groups of files, and does not attempt to move files to the beginning of the partition. Unlike the Windows built-in defragmenter tool, Contig can defragment individual files, individual directories, and subsets of the file system using wildcards.

Contig does not move any data except that belonging to the file in the question, so the amount it can defragment a file is limited to the largest contiguous block of free space on a system. Use of contig exchanges decreased file fragmentation for increased free space fragmentation.

Combined usage of the -s parameter and the wildcard symbol * allows whole directories and drives to be defragmented: for example,

will defrag all the files on hard drive C. The -s parameters means to browse directories recursively.

Directories, for example, can be defragmented with the following command. This will help speed up accessing files in a directory with many hundreds or thousands of files.