repeats

Genome Assembly Statistics

Number of scaffolds 738
Total size of scaffolds 123,846,405
Longest scaffold 2,006,230
Shortest scaffold 3,822
Number of scaffolds > 1K nt 738
Number of scaffolds > 10K nt 728
Number of scaffolds > 100K nt 344
Number of scaffolds > 1M nt 7
Number of scaffolds > 10M nt 9
Read more about Genome Assembly Statistics>

Repeat Explorer of TN20

RepeatExplorer is an online tool that can give a bioinformatician a grasp on what repeats are in a genome, as well as their relative abundance.  Here, I took TN20 reads from NCBI (SRR1800548), trimmed with trimmomatic, converted to fasta with the fastx-toolkit, and sorted and interlaced with seqtk.  200,000 reads were retained that maintained the maximum length (150bp) and had a full length mate. Classified repeats were also obtained from running RepeatModeler on the H. glycines genome [1]. Read more about Repeat Explorer of TN20

Subscribe to RSS - repeats