High-throughput sequencing technologies have strongly impacted microbiology, providing a rapid and cost-effective way of generating draft genomes and exploring microbial diversity. However, sequences obtained from impure nucleic acid preparations may contain DNA from sources other than the sample. Those sequence contaminations are a serious concern to the quality of the data used for downstream analysis, causing misassembly of sequence contigs and erroneous conclusions. Therefore, the removal of sequence contaminants is a necessary and required step for all sequencing projects.
Programs search nucleotide databases by using a nucleotide query. BLASTN key features are searching with short sequencing and cross-species comparison. Users can select an optimization according to: (i) highly similar sequences, (ii) more dissimilar sequences or (iii) somewhat similar sequences. This web application proceeds by searching sets in NCBI data sources.
Removes any sequence highly similar to a given list of vectors, adaptors, primers, or linker sequences. SeqClean was created to clean databases when specific vector and splice site data are not available. It processes the input sequence file and filters its content. The tool was compared to LUCY and cross_match and shows higher performances. It can be useful to remove vector from Expressed Sequence Tag (EST) or genomic sequences.
Finds segments of a nucleic acid sequence that could be of vector origin. VecScreen helps researchers to identify and remove any segments of vector origin before they analyse or submit sequences. It searches a query sequence for segments that correspond any sequence in a specialized non-redundant vector database. The tool categorizes vector sequences according to the strength of the match and displays their locations.
Computes nucleotide misincorporation and fragmentation patterns using next-generation sequencing reads mapped against a reference genome. mapDamage 2.0 that extends the original features of mapDamage by incorporating a statistical model of DNA damage.