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9.1 years ago
khmkhm87
•
0
I have some questions for my Whole Genome Sequences on Illumina Miseq (150bp; paired-end) platform. Since the size of Illumina Miseq was 150bp, I have a lot of reads in raw fastq files. I trimmed the sequence based on the Phred score, quality, and sequence length, and assembled with Abyss, but still the number of contigs is too many (13173), so I was not able to upload the contig file to Annotation server (RAST). Would you give me some suggestions that I can reduce my contig number by using Abyss or different assembly software? Your suggestions would be appreciated it. Thank you.
Koo.
What genome are you assembling? What is its size? What is your estimated coverage? Please report the output of `abyss-fac` on your unitigs, contigs and scaffolds FASTA files. You should be able to find these numbers also in the file `${name}-stats.tsv`.