DeconSeq categorizes possible contamination sequences, eliminates redundant hits with higher similarity to non-contaminant genomes, and provides graphical visualizations of the alignment results and classifications.
Low quality sequences, transposable element and putative contamination sequences were filtered (see Methods S1).
Contigs and scaffolds are typically filtered from the assembly if there is evidence for organellar contamination, sequencing artifacts (e.g., bacterial and phage cloning vectors), and/or prokaryotic contamination.
Multi-marker barcoding provides an a posteriori double-check for contamination, sequencing errors or mitochondria-specific pitfalls (e.g., the presence of numts or mitochondrial introgression), and the idiosyncrasies of individual markers [ 16, 56].
P. ulmi contigs containing more than 10%% of unassigned nucleotides (N) or more than 14 Ns in a row (1630 sequences) and contigs that were shorter than 200 nt after removal of vector contamination sequences (2 contigs) were not uploaded to the TSA Database following database submission procedures.
The high number of reads mapping to introns have been reported in other RNA-seq analysis [ 38] and could be due to genomic DNA contamination, sequencing of pre-mRNA, novel exons, or nascent transcription and co-transcriptional splicing as described in Ameur et al [ 39].
In order to avoid the classification of non-contaminating sequences as contamination, all possible contamination can be compared to a second set of databases and marked accordingly.
Here, we review recent developments and the challenges need to be addressed in single-cell metagenomics, including potential contamination, uneven sequence coverage, sequence chimera, genome assembly and annotation.
In order to avoid the classification of non-contaminating sequences as contamination, all possible contaminating sequences can be compared to alternative databases ("retain" databases) and matches above the thresholds are marked accordingly with "Hit to both".
