<p>You may combine all your transcriptomes into a single file and then apply a clustering method to group very similar transcripts into a single one. For that purpose, you may try <a href="http://weizhongli-lab.org/cd-hit/" rel="nofollow noreferrer">CD-HIT-EST</a> or <a href="https://github.com/soedinglab/MMseqs2" rel="nofollow noreferrer">MMseqs2</a>. For each identity threshold you are going to test, you may assess the final quality with BUSCO or by blasting against reference sequences.</p>

CC BY-SA 4.0
2020-07-20T05:06:47.130Z
2020-07-20T05:06:47.130Z
thomas duge de bernonville
<p>A simple option would be to simply supply SPAdes with some contigs that you like with <a href="http://cab.spbu.ru/files/release3.11.1/manual.html" rel="nofollow noreferrer">the <code>--trusted-contigs</code> option</a>.</p>
<p>There exist tools specifically addressing the problem of merging transcriptome assemblies. I am unsure whether this is notably different from genome assemblies sufficiently that they are better than the genome assembly mergers. Here is a partial list:</p>
<ol>
<li><a href="https://github.com/cboursnell/transfuse" rel="nofollow noreferrer">transfuse</a></li>
<li><a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1406-x" rel="nofollow noreferrer">this paper</a></li>
<li><a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0091776" rel="nofollow noreferrer">this paper</a></li>
<li><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7188282/" rel="nofollow noreferrer">this paper</a></li>
<li><a href="http://www.sigenae.org/drap" rel="nofollow noreferrer">DRAP</a></li>
</ol>
<p><a href="https://academic.oup.com/gigascience/article/8/5/giz039/5488105" rel="nofollow noreferrer">This paper</a> seems to have some more information on comparing tools, though it is not focused specifically on merging.</p>
<p>See also <a href="http://seqanswers.com/forums/showthread.php?t=38882" rel="nofollow noreferrer">the SeqAnswers</a> on this topic, and <a href="https://groups.google.com/forum/#!topic/trinityrnaseq-users/Rt9Wnrs3k0A" rel="nofollow noreferrer">this discussion too</a>.</p>

CC BY-SA 4.0
2020-07-20T05:34:49.933Z
2020-07-20T05:34:49.933Z
Maximilian Press
<p>I am building a <em>De Novo</em> transcriptome reference assembly for an eukaryotic organism for which I have a genome.</p>
<p>I've created several assemblies with rnaSpades using different kmer sizes (19 to 69 with step 10). Now I would like to merge them into one final transcriptome.</p>
<p>How could I do that?</p>
<p>Is using a genome assembly reconciliation tool such as metassembler a good idea?</p>

CC BY-SA 4.0
2018-07-16T23:07:32.643Z
Do you have a genome for the species you have data for?
conchoecia
CC BY-SA 4.0
2018-07-18T00:49:13.067Z
@conchoecia I do have a genome, although it's only a draft genome. I'm currently using it to compare the quality of my assemblies
Pitagoras Alves
CC BY-SA 4.0
2020-08-20T12:43:10.840Z
Possible? Sure, but there is a danger in doing meta-assembling. BUSCO is an ever-increasing score - if you merge multiple assemblies it will always improve because it's not really telling you much about false positives. I am not sure what do you want to use the transcriptome assembly for, but those won't ever be perfect and loads of effort might lead to only a marginaly better transciptome.
Kamil S Jaron
<assembly><transcriptome>
Merge / Reconciliate several de novo transcriptome assemblies with different kmers
# Merge / Reconciliate several de novo transcriptome assemblies with different kmers

(Asked by: username_0 on 2018-07-10)

I am building a *De Novo* transcriptome reference assembly for an eukaryotic organism for which I have a genome.

I've created several assemblies with rnaSpades using different kmer sizes (19 to 69 with step 10). Now I would like to merge them into one final transcriptome.

How could I do that?

Is using a genome assembly reconciliation tool such as metassembler a good idea?

**Tags:** assembly, transcriptome
> **Comments:**
> **username_1**: Do you have a genome for the species you have data for?  
> **username_0**: @conchoecia I do have a genome, although it's only a draft genome. I'm currently using it to compare the quality of my assemblies  
> **username_2**: Possible? Sure, but there is a danger in doing meta-assembling. BUSCO is an ever-increasing score - if you merge multiple assemblies it will always improve because it's not really telling you much about false positives. I am not sure what do you want to use the transcriptome assembly for, but those won't ever be perfect and loads of effort might lead to only a marginaly better transciptome.  

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## 2 answers

### Answer by username_3 on 2020-07-20. Score: 2

You may combine all your transcriptomes into a single file and then apply a clustering method to group very similar transcripts into a single one. For that purpose, you may try [CD-HIT-EST](http://weizhongli-lab.org/cd-hit/) or [MMseqs2](https://github.com/soedinglab/MMseqs2). For each identity threshold you are going to test, you may assess the final quality with BUSCO or by blasting against reference sequences.


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### Answer by username_4 on 2020-07-20. Score: 2

A simple option would be to simply supply SPAdes with some contigs that you like with [the `--trusted-contigs` option](http://cab.spbu.ru/files/release3.11.1/manual.html).

There exist tools specifically addressing the problem of merging transcriptome assemblies. I am unsure whether this is notably different from genome assemblies sufficiently that they are better than the genome assembly mergers. Here is a partial list:

1. [transfuse](https://github.com/cboursnell/transfuse)
2. [this paper](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1406-x)
3. [this paper](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0091776)
4. [this paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7188282/)
5. [DRAP](http://www.sigenae.org/drap)

[This paper](https://academic.oup.com/gigascience/article/8/5/giz039/5488105) seems to have some more information on comparing tools, though it is not focused specifically on merging.

See also [the SeqAnswers](http://seqanswers.com/forums/showthread.php?t=38882) on this topic, and [this discussion too](https://groups.google.com/forum/#!topic/trinityrnaseq-users/Rt9Wnrs3k0A).


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