Common noun explanations in genomic splicing

Read: The sequence produced by the high-throughput sequencing platform is called reads.

Contig: stitching software is based on the overlap area between reads, the sequence obtained by stitching is called Contig (overlapping group).

Scaffold: genome de novo sequencing, through reads splicing to obtain contigs, often also need to build 454 paired-end library or Illumina Mate-pair Library to obtain a certain size fragments (such as 3Kb, 6Kb, 10Kb, 20Kb) at both ends of the sequence. Based on these sequences, it is possible to determine the order relationship between some contig, which sequence known contigs constitute scaffold.

Contig n50 : Reads will get some different lengths of contigs after stitching. Add all the contig lengths to get a total length of contig. Then all the contigs are sorted from long to short, such as getting Contig 1,contig 2,contig 3 .... Contig 25. The Contig is added in this order, and when the added length reaches half the total length of contig, the last added contig length is contig n50. Example: Contig 1+contig Contig 3 +contig 4=contig total length *1/2, Contig 4 of the length is Contig n50. Contig n50 can be used as a judging criterion for the results of

Scaffold N50: Scaffold N50 is similar to the definition of Contig N50. Contigs stitching Assembly to obtain some different lengths of scaffolds. Add all the scaffold lengths to get a total length of scaffold. Then all the scaffolds are sorted from long to short, such as getting Scaffold 1,scaffold 2,scaffold 3 .... Scaffold 25. The Scaffold is added in this order, and when the added length reaches half the total length of Scaffold, the last added Scaffold length is Scaffold N50. Example: Scaffold 1+scaffold Scaffold 3 +scaffold 4 +scaffold 5=scaffold total length *1/2, Scaffold 5 is Scaffold N50 in length . Scaffold N50 can be used as a judging criterion for the results of genomic splicing.

Sequencing depth and coverage :

The sequencing depth refers to the ratio of the total base of the sequencing to the size of the genome to be measured. Assuming a gene size of 2M, sequencing depth of 10X, then the total amount of data obtained is 20M.

coverage refers to the proportion of the sequence obtained by sequencing to the entire genome. Due to the existence of complex structures such as high GC and repetition sequences in the genome, the sequence obtained by the final stitching Assembly of the sequencing is often unable to cover the area, which is called Gap. For example, a bacterial genome sequencing, with a coverage of 98%, then 2% of the sequence area is not obtained by sequencing.

reprinted from:http://www.majorbio.com/Tech/Htseq/403

Common noun explanations in genomic splicing