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Maq: Mapping and Assembly with Quality
By Jit 2970 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/....Software and Tools to detect structure variation with long reads !!
By Archana Malhotra 2856 days agoStructural variation caller tools using long readsfragScaff: Genome Assembly with Contiguity Preserving Transposition
By Jit 2432 days agosourceforge.net - Contiguity preserving transposition and sequencing (CPT-seq) is an entirely in vitro means of generating libraries comprised of 9216 indexed pools, each of which contains thousands of sparsely sequenced long fragments ranging from 5 kilobases to...CAMSA :: a tool for Comparative Analysis and Merging of Scaffold Assemblies
By Rahul Nayak 2569 days agohttps://cblab.org/camsa/ - CAMSA – is a tool for Comparative Analysis and Merging of Scaffold Assemblies, distributed both as a standalone software package and as Python library under the MIT license. Main features: works with any number of...Purge Haplotigs: Pipeline to help with curating heterozygous diploid genome assemblies
By Rahul Nayak 2215 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...CrossMap: program for genome coordinates conversion between different assemblies
By Rahul Nayak 1079 days ago Comments (1)crossmap.sourceforge.net - CrossMap is a program for genome coordinates conversion between different assemblies (such as hg18 (NCBI36) <=> hg19 (GRCh37)). It supports commonly used file formats...Gene Finding and Predictions
By Poonam Mahapatra 3058 days agogenome.crg.es - In this exercise, a previously annotated gene will be used to measure the accuracy of different gene finding approaches. GRAIL, GENSCAN, geneid, FGENESH, GenomeScan, GrailEXP and GENEWISE will be used to annotate the sequence. Both search by...HGT-Finder: A New Tool for Horizontal Gene Transfer Finding and Application to Aspergillus genomes
By Jit 2549 days agowww.ncbi.nlm.nih.gov - HGT-Finder: (i) can be used for HGT detection in both prokaryotes and eukaryotes, (ii) can report a statistical P value for each gene to indicate how likely it is to be horizontally transferred, and (iii) is fully automated (requires...KOBAS: a web server for gene/protein functional annotation and functional gene set enrichment
By Jit 2274 days agokobas.cbi.pku.edu.cn - KOBAS 3.0 is a web server for gene/protein functional annotation (Annotate module) and functional gene set enrichment(Enrichment module). For Annotate module, it accepts gene list as input, including IDs or sequences, and generates annotations...jobTree based python wrapper to run the genome simulation tool suite Evolver
By Jit 2588 days agogithub.com - evolverSimControl (eSC) can be used to simulate multi-chromosome genome evolution on an arbitrary phylogeny (Newick format). In addition to simply running evolver, eSC also automatically creates statistical summaries of the simulation...
