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GenomeMapper: Simultaneous alignment of short reads against multiple genomes
By Jit 2404 days ago1001genomes.org - GenomeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. It can be used to align against multiple genomes simulanteously or against a single...CSBFinder: Discovery of colinear syntenic blocks across thousands of prokaryotic genomes
By Jit 2251 days agogithub.com - CSBFinder is a standalone Desktop java application with a graphical user interface, that can also be executed via command line. CSBFinder implements a novel methodology for the discovery, ranking, and taxonomic distribution analysis of colinear...RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes
By Rahul Nayak 1697 days agogithub.com - RefKA, a reference-based approach for long read genome assembly. This approach relies on breaking up a closely related reference genome into bins, aligning k-mers unique to each bin with PacBio reads, and then assembling each bin in parallel...Published a dataset of 363 genomes from approximately 92 percent of bird families
By Jit 1495 days agoA research team published a dataset of 363 genomes from approximately 92 percent of bird families and showed the significance of sampling dense organisms for biodiversity research.OrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes
By Abhi 601 days agoorthovenn3.bioinfotoolkits.net - OrthoVenn3 is a powerful tool for comparative genomics analysis, used as a web server for full genome comparisons, annotation, and evolutionary analysis of orthologous clusters across multiple species. It has already been used by thousands of users...
Commercial and public next-gen-seq (NGS) software
Last updated 3751 days ago by Partek Comments (7)Integrated solutions CLCbio Genomics Workbench - de novo and reference assembly of Sanger, Roche FLX, Illumina, Helicos, and SOLiD data. Commercial next-gen-seq software that extends the CLCbio Main Workbench software. Includes SNP detection,...RASTtk : algorithm for building custom annotation pipelines and annotating batches of genomes
By Abhi 3162 days agohttp://rast.nmpdr.org/ - The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes...TULIP - The Uncorrected Long read Itegration Pipeline
By Jit 2587 days agogithub.com - #Running TULIP (The Uncorrected Long-read Integration Process), version 0.4 late 2016 (European eel) TULIP currently consists of to Perl scripts, tulipseed.perl and tulipbulb.perl. These are very much intended as prototypes, and additional...Purge Haplotigs: Pipeline to help with curating heterozygous diploid genome assemblies
By Rahul Nayak 2198 days agobitbucket.org - Some parts of a genome may have a very high degree of heterozygosity. This causes contigs for both haplotypes of that part of the genome to be assembled as separate primary contigs, rather than as a contig and an associated haplotig. This can be an...Environmental Genomics Group SciLifeLab/KTH Stockholm
By BioStar 753 days agohttps://github.com/envgen - Useful Metagenomics resources
