A Post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs
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 iterative approach for closing gaps in assembled...Tags: Bioinformatics, Alignment, Assembly, PAGIT, ABACAS, iCRON, RATT, IMAGE
2602 days ago
CABOG: Celera Assembler with Best Overlap Graph
CABOG (Celera Assembler with Best Overlap Graph) is scientific software for DNA research. CABOG has been a critical component of many genome sequencing projects. CABOG operates on small genomes such as bacterial as well as large genomes such as mammalian. CABOG is an extension of the Celera ...Tags: CABOG, Celera, Assembler, Overlap Graph, Bioinformatics, Assembly, Genome, Reads, NGS
2599 days ago
Tags: Bioinformatics, Steven, Salzberg, Lab, DNA, RNA, Assembly, Software, Mircobiome, NGS, Alignment, Genome
2599 days ago
Tags: Bioinformatics, Analysis, Assembly, Genome, Annotation, NCBI, Download
2599 days ago
NCBI Prokaryotic Genome Annotation Pipeline
NCBI Prokaryotic Genome Annotation Pipeline is designed to annotate bacterial and archaeal genomes (chromosomes and plasmids). Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, sma...Tags: Bioinformatics, Analysis, Assembly, Genome, Annotation, NCBI, Pipeline, Prokaryotes
2598 days ago
Tags: BIGMAC, Breaking, Inaccurate, Genomes, Merging, Assembled, Contigs, Long, Read, Metagenomic, Assembly
2592 days ago
SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology
SIMBA, SImple Manager for Bacterial Assemblies, is a Web interface for managing assembly projects of bacterial genomes. SIMBA was created to assist bioinformaticians to assemble bacterial genomes sequenced with NextGeneration Sequencing (NGS) platforms quickly, easily and effectively. SIMBA also ...Tags: SIMBA, Web, Tool, Bacterial, Genome, Assembly, Ion PGM, Sequencing
2591 days ago
How to check if fragmented set of assembly is alright ?
I assembled the genome, by fragmenting(split) the read data in TWO set. After assembling both sets, I am just wondering what to do the next? How to validate? Is that everything is going alright? I only use QUAST and it seems OK to me. Any other suggestions? Note: I assembled the genome w...Tags: NGS, Assembly, Fragmented, Split, Reads
2554 days ago
Tags: Assembly, PPT
2543 days ago