Questions tagged [repeat]

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how to repeat records in fastq n times efficiently?

How to iterate/repeat a record n times in a fastq file using bioawk? I wrote a python code using biopython, but it is very very slow. So, I am wondering if I can get some help by using bioawk. Thank ...
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Repeat analysis on eukaryotic assemblies

I have a hundred insect genomes and I'm looking for repeated regions along these assemblies. First of all, I thought of using <...
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2 votes
2 answers
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RepeatMasker annotation

I collected my own denovo library using many different tools Pipeline (structure-based ) and I updated all the headers corresponding to RepeatMasker format, to obtain Repeat coverage in the genome and ...
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Calculate the percentage of the genome that is represented by some sequences

I have construct a repeat libraries using de-novo identification methods. All results from different tools has been combined into one fasta file. How can I get the percentage of how much these ...
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4 answers
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Looking for a good tool for repeat masking in long sequences

The repeat masker site has a size limit of 90kb. Where can I mask repeats in a 500kb sequence? Ideally, I need a thorough repeat masking of known and de-novo found repeats of various complexity. I ...
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Why does repeatmasker annotate transposons of length 1?

I am working on Mac OSX. I have downloaded RepeatMasker from www.repeatmasker.org. I have downloaded RepBase from www.girinst.org. I have download the WS266 version of the C. elegans genome from ...
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4 votes
2 answers
615 views

How are centromeric/telomeric regions categorized in RepeatMasker? "Other" category?

I haven't been able to find the following in the documentation at http://www.repeatmasker.org/ (1) Why are certain regions classified as "Other"? Are these regions impossible to concretely classify ...
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18 votes
1 answer
583 views

How can I improve a long-read assembly with a repetitive genome?

I'm currently trying to assembly a genome from a rodent parasite, Nippostrongylus brasiliensis. This genome does have an existing reference genome, but it is highly fragmented. Here are some ...
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