Question: Assembly with Abyss question
gravatar for khmkhm87
4.1 years ago by
United States
khmkhm870 wrote:

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.


abyss assembly • 1.6k views
ADD COMMENTlink written 4.1 years ago by khmkhm870

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`.

ADD REPLYlink modified 4.1 years ago • written 4.1 years ago by Shaun Jackman420
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