Body: <p>I have bins from metagenomes generated with <a href="https://bitbucket.org/berkeleylab/metabat/src" rel="nofollow noreferrer">metabat2</a> on <code>bitbucket/berkleylab/scr</code> which are predicted as viral by <a href="https://github.com/laboratoriobioinformatica/MARVEL" rel="nofollow noreferrer">MARVEL</a>. <code>MARVEL</code> suggests to merge contigs with overlapping ends with <a href="http://www.phrap.org/phredphrapconsed.html" rel="nofollow noreferrer">PHRAP</a> but the documentation on the tool doesn't seem great.</p>
  <p>As it appears to be an assembler would it be okay to use another assembler? For example one of my bins has 4 contigs ~1000-5000bp in length. 3 of these seem to overlap with each other enitirely.</p>
  <hr />
  <p>I found a tool <a href="http://github.com/LANL-Bioinformatics/MeGAMerge" rel="nofollow noreferrer">MeGAMerge</a> on github which might work. Has anyone used this?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-05-10T23:06:34.907Z
Comments.Text: you could try `minimap2`.  See here: https://github.com/lh3/minimap2/blob/master/cookbook.md#read-overlap
Comments.UserDisplayName: user3479780
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-05-11T13:21:04.343Z
Comments.Text: minimap2 seems like it will not work well for my contigs as they are not that long?
Comments.UserDisplayName: Stanley Ho
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-05-11T13:23:09.647Z
Comments.Text: I found a tool called https://github.com/LANL-Bioinformatics/MeGAMerge that might work well? Anyone used it before?
Comments.UserDisplayName: Stanley Ho
Tags: <covid-19><sars-cov-2><metagenome><microbial-genomics><virus>
Title: Alternatives to phrap for merging contigs with overlapping ends?
ThreadText: # Alternatives to phrap for merging contigs with overlapping ends?
  
  (Asked by: username_0 on 2020-05-08)
  
  I have bins from metagenomes generated with [metabat2](https://bitbucket.org/berkeleylab/metabat/src) on `bitbucket/berkleylab/scr` which are predicted as viral by [MARVEL](https://github.com/laboratoriobioinformatica/MARVEL). `MARVEL` suggests to merge contigs with overlapping ends with [PHRAP](http://www.phrap.org/phredphrapconsed.html) but the documentation on the tool doesn't seem great.
  
  As it appears to be an assembler would it be okay to use another assembler? For example one of my bins has 4 contigs ~1000-5000bp in length. 3 of these seem to overlap with each other enitirely.
  
  ---
  
  I found a tool [MeGAMerge](http://github.com/LANL-Bioinformatics/MeGAMerge) on github which might work. Has anyone used this?
  
  **Tags:** covid-19, sars-cov-2, metagenome, microbial-genomics, virus
  
  > **Comments:**
  > **username_1**: you could try `minimap2`.  See here: https://github.com/lh3/minimap2/blob/master/cookbook.md#read-overlap  
  > **username_0**: minimap2 seems like it will not work well for my contigs as they are not that long?  
  > **username_0**: I found a tool called https://github.com/LANL-Bioinformatics/MeGAMerge that might work well? Anyone used it before?  
  
  ---
  
  ## 0 answers
  
  