Monday, 11 April 2016

What bacterial genome assemblers are people using?

Introduction

As of April 2016, there are about 70,000 genome assemblies in Genbank (draft and complete), with the majority being bacterial genomes. For genomes that have been submitted in NGS era, the COMMENT section of the Genbank file header has machine readable information about the sequencing technology, depth of coverage, and software used.

For example, the entry for Enterococcus faecium OC2A-1 contains this:

##Genome-Assembly-Data-START##
Finishing Goal           :: High-Quality Draft
Current Finishing Status :: High-Quality Draft
Assembly Method          :: Velvet v. 1.1.06
Genome Coverage          :: 104x
Sequencing Technology    :: Illumina
##Genome-Assembly-Data-END##

Method

I decided to parse this header for all the bacterial .gbff.gz (GenBank File Format, aka .gbk) files available at NCBI FTP to see what genome assembly software is being used for bacterial genomes. Now, like any user provided information, there is a lot of junk in this field, so I wrote some curated regexps to categorise them into cleaner bins. If more than one method was listed, I binned into Hybrid/Mixed. If if it was too minor or probably wrong I binned as Could not parse.

Results

CountAssembler Software
23725Not provided
9883AllPaths
5325Newbler
3783Velvet
3585CLC Genomics Workbench
3347Spades
2610IDBA
2477Celera Assembler
2082ABYSS
1815CLC NGS Cell
1782SOAPdenovo
1370Could not parse
1119HGAP
870MaSuRCA
853MIRA
793A5-MiSeq
308Ray
149Phred/Phrap/Consed
132Geneious
110SeqMan
109HGAP3
98Edena
69Hybrid/Mixed
59DNAstar
55Platanus
53NextGene
20Arachne
19DISCOVAR
9VelvetOptimiser
5Falcon
4Megahit
66618Total

Discussion

I was a little surprised to see ALLPATHS top the list due to its particular requirements for DNA library construction (overlapping PE + long mate pair), but the Broad Institute does do a lot of sequencing. A lot of people are using Velvet and Spades, but equal many using CLC Workbench or the NGS Cell product.

The most disturbing and funniest entries in the Could not parse division are listed below.

in-house software v. 10/18/2012
Unknown program v. before 2013-07-02
Direct Sequencing
DNASTAR SeqMan NGen v. 4.0.0
GS Reference Mapper v. September 2013
Trimmomatic v. 0.32;
Ion Torrent PGM
Artimis v. 10.1 
artimist v. 10.1
De Bruijn graph v. Apr-2011
BCFtools Consensus
BLASTN v. actual
BOWTIE v. Version 2.1.0
BWA v. 0.5.1
BioNumerics v. 6.6
ELAND alignment algorithm
Galaxy v. May 2012
de Bruijn graphs v. Mar-2013
MAQ v. 0.7.1
MATLAB v. R2013a

At the top we have in-house software (with a version number!). The Direct Sequencing could be a single perfect read of full chromosome from a really lucky Oxford Nanopore user. Is there anything Artimist (aka Artemis) cannot do? I need to upgrade my version of Trimmomatic and "actual" BLASTN too.

Conclusion

My main concern is the number of read aligners listed. There are some draft genomes myself and others have encountered where it appears the submitters have just aligned the reads to a close reference and submitted the consensus sequence as the assembly. These "genomes" sometimes cause problems in population studies, and I'd rather the reads be available instead.

7 comments:

  1. I have to check my Matlab as well for the assembler option ;-)
    Great post Torsten!

    For me also very worrying is the 35% of Not Provided... On those we can only guess and to include them in population studies can even be more dangerous. While all the assemblies published should also be published (when NCBI finally fixes their annotation and submission system and rules), raw reads is the only way to validate the data... I would reject any paper who presents assemblies without raw reads.

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    Replies
    1. It turns out that most of the 35% were done using "VelvetOptimiser" at the Sanger Institute. That metadata was somehow not required at the time of submission.

      Delete
  2. That is really interesting! I wonder if you could post the data and include taxonomy. I think it could let us see the most used assemblers per species or other taxonomic unit.

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    Replies
    1. That would be interesting Lee, but I don't have time. It was a bit of an ad hoc analysis! I know, I was naughty. Sorry.

      Delete
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    ReplyDelete