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JPred4: A Protein Secondary Structure Prediction Server
By Poonam Mahapatra 3222 days agowww.compbio.dundee.ac.uk - 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...GLEAN: an unsupervised learning system to integrate disparate sources of gene structure evidence
By Poonam Mahapatra 3067 days agosourceforge.net - GLEAN is an unsupervised learning system to integrate disparate sources of gene structure evidence (gene model predictions, EST/protein genomic sequence alignments, SAGE/peptide tags, etc) to produce a consensus gene prediction, without prior...Smudgeplot: Inference of ploidy and heterozygosity structure using whole genome sequencing data
By Neel 1703 days agogithub.com - This tool extracts heterozygous kmer pairs from kmer count databases and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovB / (CovA +...Omega2: metagenome assembly pipeline
By Jit 3394 days agoomega.omicsbio.org - Omega found overlaps between reads using a prefix/suffix hash table. The overlap graph of reads was simplified by removing transitive edges and trimming short branches. Unitigs were generated based on minimum cost flow analysis of the overlap graph...miniasm: very fast OLC-based de novo assembler for noisy long reads
By Jit 3254 days agogithub.com - Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream...MashMap: a fast and approximate software for mapping long reads (PacBio/ONT) or assembly to...
By Jit 3239 days ago Comments (1)github.com - MashMap is a fast and approximate software for mapping long reads (PacBio/ONT) or assembly to reference genome(s). It maps a query sequence against a reference region if and only if its estimated alignment identity is above a specified threshold. It...RGFA: powerful and convenient handling of assembly graphs
By Rahul Nayak 3195 days ago Comments (1)www.ncbi.nlm.nih.gov - RGFA, an implementation of the proposed GFA specification in Ruby. It allows the user to conveniently parse, edit and write GFA files. Complex operations such as the separation of the implicit instances of repeats and the merging of linear paths can...MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
By Rahul Nayak 3089 days agogithub.com - MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for single molecula sequencing (SMRT) reads. MECAT employs novel alignment and error correction algorithms that are much more efficient than the state of art of aligners and...Cerulean: A hybrid assembly using high throughput short and long reads
By Rahul Nayak 3064 days agosourceforge.net - Cerulean extends contigs assembled using short read datasets like Illumina paired-end reads using long reads like PacBio RS long reads. Cerulean v0.1 has been implemented with bacterial genomes in mind. The method is fully described in...ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole...
By Rahul Nayak 3036 days agogithub.com - ChopStitch is a new method for finding putative exons and constructing splice graphs using an assembled transcriptome and whole genome shotgun sequencing (WGSS) data. ChopStitch identifies exon-exon boundaries in de novo assembled RNA-seq data with...
