We just posted another pre-submission paper to arXiv.org:
Illumina Sequencing Artifacts Revealed by Connectivity Analysis of Metagenomic Datasets
Authors: Adina Chuang Howe, Jason Pell, Rosangela Canino-Koning, Rachel Mackelprang, Susannah Tringe, Janet Jansson, James M. Tiedje, and C. Titus Brown
Sequencing errors and biases in metagenomic datasets affect coverage-based assemblies and are often ignored during analysis. Here, we analyze read connectivity in metagenomes and identify the presence of problematic and likely a-biological connectivity within metagenome assembly graphs. Specifically, we identify highly connected sequences which join a large proportion of reads within each real metagenome. These sequences show position-specific bias in shotgun reads, suggestive of sequencing artifacts, and are only minimally incorporated into contigs by assembly. The removal of these sequences prior to assembly results in similar assembly content for most metagenomes and enables the use of graph partitioning to decrease assembly memory and time requirements.
This paper extends our partitioning paper (Pell et al, PNAS, 2012) and describes the effect of removing sequencing artifacts and highly conserved sequences from read data sets prior to partitioning large environmental metagenomes.