2638 days ago
2617 days ago
Barrnap: Bacterial ribosomal RNA predictor
Barrnap predicts the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). It tak...2610 days ago
A Post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs
PAGIT addresses the need for software to generate high quality draft genomes. It is based on a series of programs that we developed: ABACAS, that is able to contigu...2610 days ago
CABOG: Celera Assembler with Best Overlap Graph
...ng machines (Marine microbes, 2006). Today, CABOG is one of the leading assembly programs for data sets that include paired end data from the Roche 454 line of sequencing machines.2607 days ago
NCBI Prokaryotic Genome Annotation Pipeline
...homology based methods. The first version of NCBI Prokaryotic Genome Automatic Annotation Pipeline (PGAAP; see Pubmed Article) developed in 2005 has been replaced with an upg...2606 days ago
CAR: Reconstructing Contiguous Regions of an Ancestral Genome
We describe a new method for predicting the ancestral order and orientation of those intervals from their observed adjacencies in modern species. We combine the re...2604 days ago
Pollux: platform independent error correction of single and mixed genomes
...introduced by Illumina, Ion Torrent, and Roche 454 sequencing technologies and...na MiSeq errors, 88% of Ion Torrent PGM errors, 85% of Roche 454 GS Junior error...formatics.biomedcentral.com/articles/10.1186/s12859-014-0435-62603 days ago
npScarf: Scaffolding and Completing Assemblies in Real-time Fashion
...and the detection of genes from mobile elements (plasmids and genomic islands). Complete paper at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5321748/2599 days ago
SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology
...MBA also is open source tool, i.e., can be freely downloaded, shared and modified. https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1344-72599 days ago