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SimLoRD: A read simulator for third generation sequencing reads
By Aaryan Lokwani 2283 days agobitbucket.org - SimLoRD is a read simulator for third generation sequencing reads and is currently focused on the Pacific Biosciences SMRT error model. Reads are simulated from both strands of a provided or randomly generated reference sequence. The reference...Qualimap2: Evaluating next generation sequencing alignment data
By Jit 2264 days agoqualimap.bioinfo.cipf.es - Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like...sim3C: Read-pair simulation of 3C-based sequencing methodologies (HiC, Meta3C, DNase-HiC)
By Jit 2200 days agogithub.com - Required python modules biopython intervaltree numpy scipy tqdm PyYAMLjackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator
By Abhimanyu Singh 1946 days agogithub.com - jackalope simply and efficiently simulates (i) variants from reference genomes and (ii) reads from both Illumina and Pacific Biosciences (PacBio) platforms. It can either read reference genomes from FASTA files or simulate new ones. Genomic variants...MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization
By Jit 1763 days agogithub.com - MitoZ is a Python3-based toolkit which aims to automatically filter pair-end raw data (fastq files), assemble genome, search for mitogenome sequences from the genome assembly result, annotate mitogenome (genbank file as result), and mitogenome...dcGOR
By Martin Jones 3666 days agoan R package for analysing ontologies and protein domain annotationsCANU: Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing.
By Jit 3131 days ago Comments (2)github.com - Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION). The software is currently alpha level, feel free to use and report issues encountered. Canu is...MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping
By Neel 3107 days agojournals.plos.org - MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies,...GAEMR
By Jit 3082 days agowww.broadinstitute.org - The Genome Assembly Evaluation Metrics and Reporting (GAEMR) package is an assembly analysis framework composed a number of integrated modules. These modules can be executed as a single program to generate a complete...HivePlot
By Jit 2835 days agohttp://www.hiveplot.com/ - The hive plot is a rational visualization method for drawing networks. Nodes are mapped to and positioned on radially distributed linear axes — this mapping is based on network structural properties. Edges are drawn as curved links....
