Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-07-20T05:06:47.130Z
Answers.LastActivityDate: 2020-07-20T05:06:47.130Z
Answers.UserDisplayName: thomas duge de bernonville
Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-07-20T05:34:49.933Z
Answers.LastActivityDate: 2020-07-20T05:34:49.933Z
Answers.UserDisplayName: Maximilian Press
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-07-16T23:07:32.643Z
Comments.Text: Do you have a genome for the species you have data for?
Comments.UserDisplayName: conchoecia
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-07-18T00:49:13.067Z
Comments.Text: @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
Comments.UserDisplayName: Pitagoras Alves
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-20T12:43:10.840Z
Comments.Text: 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.
Comments.UserDisplayName: Kamil S Jaron
Tags: <assembly><transcriptome>
Title: Merge / Reconciliate several de novo transcriptome assemblies with different kmers
ThreadText: # 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**: @username_1 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.  
  
  ---
  
  ## 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.
  
  
  ---
  
  ### 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).
  
  
  ---
  
  