Rectangle Graph for Repeat Resolution in Genome Assembly
...fic implementation of the idea of the rectangle graph approach is already include...istribution, we're also releasing the Rectangle Graph Module (RGM) as the separat...rom the current implementation of the rectangle graph approach in SPAdes, in the...2384 days ago
3d-dna: 3D de novo assembly (3D DNA) pipeline
...o;. In addition, the pipeline uses tools and methods from Juicer (Durand & Shamim et al., Cell Systems, 2016) and Juicebox (Durand & Robinson et al., Cell...2384 days ago
JPred4: A Protein Secondary Structure Prediction Server
JPred4 (http://www.compbio.dundee.ac.uk/jpred4) is the latest version of the popular JPred protein secondary structure prediction server which provides predictions by the JNet algorithm, one of the most accurate methods for secondary structure prediction.2382 days ago
Seal: SEquence ALignment evaluation suite
...This software (implemented in Java) provides several utilities that can be used t...rom one or more FASTA files. Alternatively, generating an artificial reference g...repeat variability rate). Simulating reads from random locations in the genome b...2378 days ago
Jabba: Hybrid Error Correction for Long Sequencing Reads
...r correction tool to correct third generation (PacBio / ONT) sequencing data, using second generation (Illumina) data. Input...kes as input a concatenated de Bruijn graph and a set of sequences: th...ec/jabba/wiki https://almob.biomedcentral.com/articles/10.1186/s13015-...2045 days ago
LRCstats: Long Read Correction Statistics
...r long reads outputted by third generation sequencing technology suc...es. The reads produced by third generation sequencing technology, as...ong reads are plagued by high error rates, which can cause issues in...-way alignments using a dynamic programming algorithm. Statistics on...2376 days ago
proovread : large-scale high-accuracy PacBio correction through iterative short read consensus
proovread : large-scale high-accuracy PacBio correction through iterative short read consensus outperforms PacBioToCA/LSC in terms of accuracy and contiguity/sensitivity...s 454, ... proovread maps high coverage data to pacbio reads (bwa m...2376 days ago
zPicture: A dynamic blastz alignment visualization
zPicture is a dynamic alignment and visualization tool that is based on blastz alignment program utilized by PipMaker. zPicture alignments can be automatically submitted to rVista 2.0 to identify conserved transcription factor binding sites.2350 days ago
2374 days ago
Alien_Hunter : prediction of putative Horizontal Gene Transfer (HGT) events
..._hunter is an application for the prediction of putative Horizontal Gene Transfer (HGT) events with the im...2-state 2nd order Hidden Markov Model (HMM), in a change-point detection framework, to optimize the locali...2373 days ago