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NanoPack: visualizing and processing long-read sequencing data
By Jit 2779 days agogithub.com - The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are compatible...Circlator: automated circularization of genome assemblies using long sequencing reads
By Poonam Mahapatra 3004 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...SimLoRD: A read simulator for third generation sequencing reads
By Aaryan Lokwani 2905 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...LoRMA: a tool for correcting sequencing errors in long reads such those produced by Pacific...
By Jit 3702 days agowww.cs.helsinki.fi - LoRMA is a tool for correcting sequencing errors in long reads such those produced by Pacific Biosciences sequencing machines. Publication: L. Salmela, R. Walve, E. Rivals, and E. Ukkonen: Accurate selfcorrection of errors in long reads using de...Jabba: Hybrid Error Correction for Long Sequencing Reads
By Jit 3134 days agogithub.com - Jabba is a hybrid error correction tool to correct third generation (PacBio / ONT) sequencing data, using second generation (Illumina) data. Input Jabba takes as input a concatenated de Bruijn graph and a set of sequences: the de Bruijn graph...Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput...
By Jit 3030 days agogithub.com - Heap, that enables robustly sensitive and accurate calling of SNPs, particularly with a low coverage NGS data, which must be aligned to the reference genome sequences in advance. To reduce false positive SNPs, Heap determines genotypes and calls...P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads
By Jit 2976 days agowww.fishbrowser.org - P_RNA_scaffolder, a fast and accurate tool using paired-end RNA-sequencing reads to scaffold genomes. This tool aims to improve the completeness of both protein-coding and non-coding genes. After this tool was applied to scaffolding human contigs,...RapClust: Accurate, Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence...
By Rahul Nayak 2861 days agogithub.com - RapClust is a tool for clustering contigs from de novo transcriptome assemblies. RapClust is designed to be run downstream of the Sailfish or Salmon tools for rapid transcript-level quantification. Specifically,...FERMI
By Jit 3617 days agogithub.com - Fermi is a de novo assembler with a particular focus on assembling Illumina short sequence reads from a mammal-sized genome. In addition to the role of a typical assembler, fermi also aims to preserve heterozygotes which are...Hapsembler: An Assembler for Highly Polymorphic Genomes
By Jit 2997 days agocompbio.cs.toronto.edu - Hapsembler is a haplotype-specific genome assembly toolkit that is designed for genomes that are rich in SNPs and other types of polymorphism. Hapsembler can be used to assemble reads from a variety of platforms including Illumina and Roche/454....
