14
votes
Are there any RepBase alternatives for genome-wide repeat element annotations?
Dfam has recently launched a sister resource, Dfam_consensus, whose stated aim is to replace RepBase. From the annoucement:
Dfam_consensus provides an open framework for the community to store both ...
- 4,845
7
votes
Are there any RepBase alternatives for genome-wide repeat element annotations?
For pre-existing reliabe TE libraries it is a bit of a mess, because not everybody deposits the species-specific TE libraries to a database like RepBase. And as far as I know DFAM contains only human ...
- 71
6
votes
Counting repeated kmers sequences that match at least x % of reads sequence
The following javascript does what you want. You need node.js to run it. It should be easy to translate the code to Python. I have not carefully tested it. Use with caution.
EDIT (response to new ...
- 6,485
6
votes
Accepted
How can I use Nanopore reads to close gaps or resolve repeats in a short-read assembly?
You might want to look into Unicycler (manuscript with more information can be found here); even though it is supposed to be used with bacterial genomes only, it might work well with a small genome ...
- 967
5
votes
Are there any RepBase alternatives for genome-wide repeat element annotations?
You could use RepeatScout, which has defined repeat libraries for a limited number of species (including human, mouse, and rat). If your taxon is not represented, you can also do de novo repeat ...
- 3,928
4
votes
Are there any RepBase alternatives for genome-wide repeat element annotations?
AFAIK Dfam and Repbase are currently the two best sources of (a variety of) TE sequences.
In my genome annotations I have used RepeatModeler+RepeatMasker and then later used Repbase+tblastx and Dfam+...
- 184
4
votes
Accepted
What does "motif 2 bp or longer" mean?
What's your reference for the definition of STRs? I think it is still ambiguous among the community. Wikipedia states motifs of >=2 bp. However other references include homopolymers as well:
Source 1, ...
4
votes
Accepted
Is it wise to use RepeatMasker on prokaryotes?
If I understood correctly your question, you want to mask those regions in a (FASTA?) genome. I think you could identify those regions using mummer and mask them using bedtools.
...
- 967
4
votes
Looking for a good tool for repeat masking in long sequences
RepeatMasker can downloaded an run locally. There's then no size limit, though do note that it's quite slow for mammalian-sized sequences (you'll want to split it into chunks and run in parallel in ...
- 19.6k
3
votes
Annotatation of transposable elements / transposons / SINE sequences in human
repeatmasker is meant to annotate/mask a genome given a library of known transposable elements. From the project description, I assume you have not done any sequencing on your own. Then, instead of ...
- 5,517
3
votes
Accepted
Finding 2000 bp sequences that occur more than once in the genome
MUMmer includes a repeat-match tool which can do exactly that:
...
- 810
3
votes
Looking for a good tool for repeat masking in long sequences
RepeatFinder may suffice by Volfovsky et al. (2001) and is available for download.
- 31
3
votes
Accepted
Is there any way to align ChIP-seq reads to telomeres?
This paper https://www.biorxiv.org/content/10.1101/728519v1.full examines the mapping of some human telomeric sequences, and indicates that there is something like 130kb missing at the telomeres in ...
- 1,012
3
votes
Finding transposable elements using RepeatMasker
You need to model the repeats in your de novo genome.
See:
http://www.repeatmasker.org/RepeatModeler/ and
https://www.biostars.org/p/154290/ (from previous answer)
You first build a database named "...
- 1,573
3
votes
Accepted
TRAL does not find "Phobos result file"
TRAL 0.3.5 has bugs running and parsing Phobos. You can follow progress towards a fix on this issue: https://github.com/acg-team/tral/issues/16
Until the issue is fixed, you should remove Phobos from ...
- 146
3
votes
Are there any RepBase alternatives for genome-wide repeat element annotations?
+1 for taking issue with RepBase.
I use the annotations from the Hammell Lab GTFs that they put out with TEtoolkit. It is similar to what you described to be using so this may be a redundant and ...
3
votes
Accepted
Finding the location and unit length of repetitive sequences within a long read
I've sorted the visualisation out. Here are three alternative representations of repetitive structures for the same sequence:
These were generated using the same R script, callable from the command ...
- 13.8k
2
votes
Finding the location and unit length of repetitive sequences within a long read
It could be an idea to fragment the long reads into small sequences, like simulating Illumina reads of 150 bp, and then map these small sequences against the original long reads and extract regions ...
- 141
2
votes
Are there any RepBase alternatives for genome-wide repeat element annotations?
I know this question is a bit old, but this is still an issue for a lot of researchers not being able to access RepBase. It seems now that the most recent version of RepeatMasker is dependent upon ...
- 21
2
votes
Accepted
Finding transposable elements using RepeatMasker
That's one answer ^, not sure if you NEED to do that, which wouldn't actually classify your elements as LTRs, it would just find repetitive sequences in your new genome (as you discovered).
To get ...
- 184
2
votes
Aligning ChIP-Seq reads to repeats for downstream peak analysis
This is very good question, but as far as I know there really isn't a good answer. I will attempt to provide some comments and tips.
However, I'm trying to do similar with a dataset which may ...
2
votes
Looking for a good tool for repeat masking in long sequences
From: http://meme-suite.org/doc/glam2_tut.html, here's a few tools that do various repeat masking tasks.
These tools mask various kinds of repeats: Repeatmasker, Censor, seg/pseg/nseg, DUST,
...
- 66
2
votes
RepeatMasker annotation
RepeatMasker comes with a buildSummary.pl script.
You can input the .out file from your RepeatMasker run and there is a flag to enter your species
e.g.
...
- 31
2
votes
Is there a "definitive" database for Mobile Genetic Elements?
Would advise doing Denovo identification method structure-based. Then use these public databases ( RepBase, Dfam ) to look for high similarity or homology exploration, this possibility if your ...
- 374
1
vote
Are there any tools for discovering tandem repeats around a variant in a VCF file?
The old program for doing this last updated in 2016 is Tandem Repeat Finder (TRF) here. This will not find a microsatellite sequence at a given variant, but instead find all tandem repeats in the ...
M__♦
- 11.9k
1
vote
Accepted
Are there any tools for discovering tandem repeats around a variant in a VCF file?
After researching a bit, I found a couple of tools that take as input BAM files. I did not test them yet:
GangSTR
lobSTR
hipSTR
Tandem Repeat Finder (thanks to Michael G.'s answer)
If I find more ...
- 1,105
1
vote
Is there a "definitive" database for Mobile Genetic Elements?
Back in the Day™ RepeatMasker[1] was the go-to tool everyone used for TE annotation in eukaryotes. At the time, the RepBase database from GIRI[2] (license required) was the de facto database ...
- 5,060
1
vote
Accepted
RepeatMasker annotation
After long years of just conceptual knowledge of what the software does, I was dealing with RepearMasker this week. So, I am not entirely sure I am correct, but ...
- 5,517
1
vote
Finding transposable elements using RepeatMasker
In case someone finds this years later: OP's problem was the use of the "-noint" flag. It stands for "no interspersed", so the OP explicitly asked RepeatMasker NOT to look for ...
- 11
1
vote
Is it wise to use RepeatMasker on prokaryotes?
From your comment, it seems that masking regions are not your priority, but you would rather find them (correct me if I am wrong):
not interested in masking, but really finding any type of repeats, ...
- 2,676
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