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Cotton genome sequence & assemblies



The Udall lab has run one lane of A-genome cotton (A2-44) on Illumina's HiSeq system. The run was 100 bp x 2 paired ends. The two original output files have been split into 6 smaller files for downloading convenience below. The "_1_" and "_2_" refer to forward and reverse reads respectively.

The following files--soapA1_45.scafSeq and soapA2_45.scafSeq--are de novo assemblies of WGS data from Gossypium herbaceum (A1-155) and G. arboreum (A2-1011). Both accessions were sequenced at about 45x coverage with 100 bp paired-end Illumina reads. The raw reads are available from SRA under PRJNA202236 and PRJNA202235. Reads were trimmed with sickle using a minimum quality threshold of 20, then assembled with SOAPdenovo using a Kmer size of 45. Please cite the following paper in reference to the sequence data:
Page JT, Huynh MD, Liechty ZS, Grupp K, Stelly DM, Hulse AM, Ashrafi H, Van Deynze A, Wendel JF, Udall JA: Insights into the Evolution of Cotton Diploids and Polyploids from Whole-Genome Re-sequencing. G3 (Bethesda) 2013.


We welcome your comments and suggestions.