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