I need one page to collate software and docs I come across, and that is or might be useful to me. Let’s hope this does not become a total mess, and would be useful to others.

Short read assembly:

Nick Loman’s xbase. For short read annotation and assembly. This goes hand in hand with his sage advice page. Also, this document from Illumina

Velvet, of course. De-novo assemblies.

Standardized velvet assembly report from Jeremy Leipzig.

MetaVelvet for metagenomic assemblies.

MIRA for scaffolded assemblies.



Annotation resources:

RAST & MG-RAST for genomes and metagenomes respectively.

Microbial ecology:

QIIME from Rob Knight’s lab

Mothur from Pat Schloss’s lab.

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One Response to “Resources”

  1. Unum says:

    Hi there! I was doing some Saturday reading on my favorite subject of smORFs and I came across your entry
    I’m a PhD student at the Couso lab at the University of Sussex and I wanted to correct the collaboration. Thanks for highlighting the importance of the small genes we work with. The discovery of the first smORF in Drosophila (tal) was pure chance and we are now well underway with characterising others that have been found as a result of the pipeline in question – and it looks pretty good. Stay tuned for more results! (fingers crossed) 🙂
    Cheers! I really enjoyed browsing your blog.

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