Jit
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A Post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs
By Abhimanyu Singh 3374 days agowww.sanger.ac.uk - PAGIT addresses the need for software to generate high quality draft genomes. It is based on a series of programs that we developed: ABACAS, that is able to contiguate contigs from a de novo assembly against a closely related reference. IMAGE, an...HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution
By Jit 3103 days agogithub.com - Software accompanying "HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution" Preprint: http://biorxiv.org/content/early/2016/08/01/062117 Paper: http://genome.cshlp.org/content/27/5/747.full An ipython notebook to...EvidentialGene: tr2aacds, mRNA Transcript Assembly Software
By Rahul Nayak 3013 days agoarthropods.eugenes.org - EvidentialGene is a genome informatics project, "Evidence Directed Gene Construction for Eukaryotes", to construct high quality, accurate gene sets for animals and plants, developed by Don Gilbert at Indiana University,...GRAbB: Selective Assembly of Genomic Regions, a New Niche for Genomic Research
By Rahul Nayak 2749 days agogithub.com - GRAbB is shown to be more efficient than MITObim in terms of speed, memory and disk usage. The other functionalities (handling multiple targets simultaneously and extracting homologous regions) of the new program are not matched by other programs....Consed--A Finishing Package (BAM File Viewer, Assembly Editor, Autofinish, Autoreport, Autoedit,...
By Neel 2373 days agowww.phrap.org - Supports Illumina, 454, other Next-Gen and Sanger Reads and allows mixtures of these read types Consed includes BamScape which can view bam files with unlimited numbers of reads. BamScape can bring up consed to edit reads and the reference sequence...CLAW: Chloroplast Long-read Assembly Workflow
By LEGE 898 days agogithub.com - CLAW (Chloroplast Long-read Assembly Workflow) is an mostly-automated Snakemake-based workflow for the assembly of chloroplast genomes. CLAW uses chloroplast long-reads, which are baited out of larger read libraries (e.g., an Oxford Nanopore...PGAP-X: Extension on pan-genome analysis pipeline
By Rahul Nayak 3118 days agohttps://pgapx.ybzhao.com/ - PGAP-X is a microbial comparative genomic analysis platform with graphic interface. Serials of algorithms and methodologies have been developed and integrated to analyze and visualize genomics structure variation, gene distribution with different...Tigers genome sequenced
By Rahul Agarwal 4706 days agoOnly 4.4 percent DNA difference between Tiger and house catsOpera: An optimal genome scaffolding program
By Jit 3175 days agosourceforge.net - Opera (Optimal Paired-End Read Assembler) is a sequence assembly program (http://en.wikipedia.org/wiki/Sequence_assembly ). It uses information from paired-end or long reads to optimally order and orient contigs assembled from...
