Results for "R"
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Enrichr: a comprehensive gene set enrichment analysis
Enrichment analysis is a popular method for analyzing gene sets generated by genome-wide experiments. Here we present a sign...tools in this domain called Enrichr. Enrichr currently contai...iological knowledge for further biological discoveries. Enric...2624 days ago
- NGS data are just a bunch of sequences, you have no idea which region in the genome each sequences comes from, which gene it represents.....to align the sequences to the reference sequence. The referen...es not map an equal amount of reads to the correct position i...
2619 days ago
- FASTQ format is a text-based format for storing both a biological sequenc...sp;nucleotide sequence) and its corresponding quality scores. Bot...with a single ASCII character for brevity. It was ori...for storing the output of high-throughput sequencing instruments...
2618 days ago
- A tetra-nucleotide is a fragment of DNA sequence with 4 bases (e.g. AGTC or TTGG). Pride et al. (2003) showed that the frequency of tetra-nucleotides in...genetic signals. Even though tetra-nucleotide analysis (TNA) ut...useful for phylogenetic characterization when whole genome...
2617 days ago
- SSPACE standard is a stand-alone program for scaffolding pre-assembled contigs using NGS pai...d-read data. It is unique in offering the possibility to manuall...e information of paired-end and/or matepair data, SSPACE is able...tig sequences (FASTA) and NGS paired-read data (Illumina/454/Sol...
2616 days ago
CLA: Contig-Layout-Authenticator
To improve upon the shortcomings associated with the construction of draft genomes with Illumina paired-end sequencing, we develope...The CLA pipeline can scaffold reference-sorted contigs based...gle command line input to generate ordered scaffolds. Script...2616 days ago
- This tutorial will serve as an example of how to use free and open-source genome assembly and secondary scaffolding tools to generate high...sp;bacterial sequence data. The bacterial sample used in this tutori...aning that there are forward and reverse reads, which we will design...
2616 days ago
Barrnap: Bacterial ribosomal RNA predictor
Barrnap predicts the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5...rite GFF3 as output. It uses the new NHMMER tool that comes with HMMER 3....2609 days ago
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 develo...vo assembly against a closely related reference. IMAGE, an i...ese software and makes them more accessible for users.2609 days ago
CABOG: Celera Assembler with Best Overlap Graph
CABOG (Celera Assembler with Best Overlap Graph) is scientific software for DNA research. CABOG has...of the Celera Assembler software that was originally develope...; CABOG is one of many software programs called genome assem...the first to assemble both parental haplotypes of one human...2606 days ago
