#UCDAssemble Workshop - Friday Update

#UCDAssemble Workshop - Friday Update

The workshop is not over yet. In this commentary, we will add topics that did not fit yesterday’s coverage. It will be updated, as we go through various tweets.

Lex Nederbragt - Assembly: before and after

These slides contain set of pre- and post-processing tools for genome assembly.

** Assembly: before and after ** from Lex Nederbragt

Jared Simpson discussed Paul Melsted’s Quick and Dirty de Bruijn Code

You can access the code from following link.

Naive python implementation of a de Bruijn Graph

De Bruijn graphs are widely used in assembly algorithms and I guess writing your own assembler is a rite of passage. Hoping to get some answers I got this question from Mick Watson. Since I had a script lying around that I used for validation I thought I would share it.


@Dr_Bik discussed PhyloSift, which is useful for placing sequences on guide phylogenetic trees.

Systematic identification of gene families for use as markers for phylogenetic and phylogeny- driven ecological studies of bacteria and archaea and their major subgroups

With the astonishing rate that the genomic and metagenomic sequence data sets are accumulating, there are many reasons to constrain the data analyses. One approach to such constrained analyses is to focus on select subsets of gene families that are particularly well suited for the tasks at hand. Such gene families have generally been referred to as marker genes. We are particularly interested in identifying and using such marker genes for phylogenetic and phylogeny-driven ecological studies of microbes and their communities. We therefore refer to these as PhyEco (for phylogenetic and phylogenetic ecology) markers. The dual use of these PhyEco markers means that we needed to develop and apply a set of somewhat novel criteria for identification of the best candidates for such markers. The criteria we focused on included universality across the taxa of interest, ability to be used to produce robust phylogenetic trees that reflect as much as possible the evolution of the species from which the genes come, and low variation in copy number across taxa. We describe here an automated protocol for identifying potential PhyEco markers from a set of complete genome sequences. The protocol combines rapid searching, clustering and phylogenetic tree building algorithms to generate protein families that meet the criteria listed above. We report here the identification of PhyEco markers for different taxonomic levels including 40 for all bacteria and archaea, 114 for all bacteria, and much more for some of the individual phyla of bacteria. This new list of PhyEco markers should allow much more detailed automated phylogenetic and phylogenetic ecology analyses of these groups than possible previously.

Nick Loman - CONCOCT

Nick Loman presented on CONCOCT. Readers can access the paper from following link.

CONCOCT: Clustering cONtigs on COverage and ComposiTion

Metagenomics enables the reconstruction of microbial genomes in complex microbial communities without the need for culturing. Since assembly typically results in fragmented genomes the grouping of genome fragments (contigs) belonging to the same genome, a process referred to as binning, remains a major informatics challenge. Here we present CONCOCT, a computer program that combines three types of information - sequence composition, coverage across multiple sample, and read-pair linkage - to automatically bin contigs into genomes. We demonstrate high recall and precision rates of the program on artificial as well as real human gut metagenome datasets.

The Most Profound Advice Given in #UCDAssemble

If you cannot make things work, send the paper to Nature :)

Written by M. //