3020 days ago
Trimmomatic: A flexible read trimming tool for Illumina NGS data
...DING:3) Remove trailing low quality or N bases (below quality 3) (TRAILING:3) Scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below...2957 days ago
2868 days ago
Comparative genomics educational material and papers bookmarks
...specific EBRs (100) reported earlier using a slightly lower resolution (500 kilobases (kb)), indicating that both lineages evolved with an average rate of ~2.1 large-scale rear...2748 days ago
QuorUM: An Error Corrector for Illumina Reads
...latively short (most often 100 bp to 150 bp) reads at a low cost. Even with low (advertised 1%) error rate, 100 × coverage Illumina data on average has an error in some read at...2385 days ago
2188 days ago
FastANI: fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI)
FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared...2137 days ago
REVIGO: Reduced Visualize gene ontology
REViGO can take long lists of Gene Ontology terms and summarize them by removing redundant GO terms. The remaining terms can be visualized in semantic similarity-based...2120 days ago
ANItools web: a web tool for fast genome comparison within multiple bacterial strains
...s a software package written by PERL scripts that can be run in a Linux/Unix system. If you want to compare bacterial genomes and calculate their average nucleotide identity (ANI), yo...2014 days ago
OrthoANI: An improved algorithm and software for calculating average nucleotide identity
OAT uses OrthoANI to measure the overall similarity between two genome sequences. ANI and OrthoANI are comparable algorithms: they share the same species demarcation cu...1986 days ago