BOL

github.com - medaka is a tool to create a consensus sequence from nanopore sequencing data. This task is performed using neural networks applied from a pileup of individual sequencing reads against a draft assembly. It outperforms graph-based methods...

A core element in the downstream analysis for RNA-seq data involves the translation of assembled sequences into their corresponding amino acid sequences, and on the nucleotide level into the protein coding sequences (CDS) not containing any...

www.ncbi.nlm.nih.gov - Tbl2asn is a command-line program that automates the creation of sequence records for submission to GenBank. It uses many of the same functions as Sequin but is driven generally by data files. Tbl2asn generates .sqn files for submission to GenBank....

github.com - Scripts for the analysis of HGT in genome sequence data

emboss.sourceforge.net - needleall reads a set of input sequences and compares them all to one or more sequences, writing their optimal global sequence alignments to file. It uses the Needleman-Wunsch alignment algorithm to find the optimum alignment (including gaps) of two...

www.nature.com - Segmental Duplication Assembler (SDA; https://github.com/mvollger/SDA) constructs graphs in which paralogous sequence variants define the nodes and long-read sequences provide attraction and repulsion edges, enabling the partition and assembly of...

genomebiology.biomedcentral.com - The well-established inaccuracy of purely computational methods for annotating genome sequences necessitates an interactive tool to allow biological experts to refine these approximations by viewing and independently evaluating the data supporting...

On Jan 10 2020, while news of the first fatality was barely trickling in, the 29,903 letters constituting the viral genome from an affected individual in Wuhan had already been elucidated (even though a few corrections were made subsequently).

Submit your SARS-CoV-2 sequence data to GenBank and SRA with our new submission landing page.

github.com - MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin)...