BioStar
Bioinformatician
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Bandage: interactive visualization of de novo genome assemblies
By Shruti Paniwala 2545 days agorrwick.github.io - Bandage (a Bioinformatics Application for Navigating De novo Assembly Graphs Easily) is a tool for visualizing assembly graphs with connections. Users can zoom in to specific areas of the graph and interact with it by moving nodes,...MITOS: improved de novo metazoan mitochondrial genome annotation
By Jit 2219 days agomitos.bioinf.uni-leipzig.de - Allows automatic annotation of metazoan mitochondrial genomes. MITOS is a pipeline designed to compute a consistent de novo annotation of the mitogenomic sequences. The software allows for a systematic error screening, the standardisation of gene...Integrative Meta-Assembly Pipeline (IMAP): Chromosome-level genome assembler combining multiple de...
By Jit 1910 days agojournals.plos.org - Chromosome-level genome assembler combining multiple de novo assemblies https://github.com/jkimlab/IMAPDFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication
By Jit 2565 days agohttps://dfast.nig.ac.jp/ - We developed a prokaryotic genome annotation pipeline, DFAST, that also supports genome submission to public sequence databases. DFAST was originally started as an on-line annotation server, and to date, over 7,000 jobs have been processed since its...Circlator: automated circularization of genome assemblies using long sequencing reads
By Poonam Mahapatra 2383 days agosanger-pathogens.github.io - A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology manuscript. Citation: "Circlator: automated circularization of genome assemblies using long sequencing reads", Hunt et al, Genome Biology...P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads
By BioStar 2268 days agowww.fishbrowser.org - P_RNA_scaffolder is a novel scaffolding tool using Pair-end RNA-seq to scaffold genome fragments. The method is suitable for most genomes. The program could utilize Illumina Paired-end RNA-sequencing reads from target speciesies. Our method provides...Maq: Mapping and Assembly with Quality
By Jit 2922 days agomaq.sourceforge.net - Maq stands for Mapping and Assembly with Quality It builds assembly by mapping short reads to reference sequences. Maq is a project hosted by SourceForge.net. The project page is available athttp://sourceforge.net/projects/maq/....BIMA V3: an aligner customized for mate pair library sequencing
By Abhimanyu Singh 2900 days agobioinformatics.oxfordjournals.org - Summary: Mate pair library sequencing is an effective and economical method for detecting genomic structural variants and chromosomal abnormalities. Unfortunately, the mapping and alignment of mate pair read pairs to a reference genome is a...Software and Tools to detect structure variation with long reads !!
By Archana Malhotra 2809 days agoStructural variation caller tools using long readsLoRDEC: a hybrid error correction program for long, PacBio reads
By Jit 2783 days agowww.atgc-montpellier.fr - LoRDEC is a program to correct sequencing errors in long reads from 3rd generation sequencing with high error rate, and is especially intended for PacBio reads. It uses a hybrid strategy, meaning that it uses two sets of reads: the reference read...
