Results for "NGS"
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SGA is a de novo genome assembler based on the concept of string graphs. The major goal of SGA is to be very memory efficient, which is achieved by using a compressed representation of DNA sequence reads. More at https://github.com/jts/sga SGA dependencies: -google sparse hash library (http://...Tags: Bioinformatics, Analysis, Assembly, Genome, SGA, NGS
2716 days ago
- fqtools is a software suite for fast processing of FASTQ files. Various file manipulations are supported. See below for a full list of the subcommands available and a brief description of their purpose. Most of the individual subcommands will take either a single file or a pair of ...
Tags: Bioinformatics, Analysis, NGS, fqtools, FASTQ
2715 days ago
e-RGA: enhanced Reference Guided Assembly of Complex Genomes
Next Generation Sequencing has totally changed genomics: we are able to produce huge amounts of data at an incredibly low cost compared to Sanger sequencing. Despite this, some old problems have become even more difficult, de novo assembly being on top of this list. Despite efforts to design tool...Tags: Bioinformatics, Analysis, NGS, e-RGA, Genome, Assemble
2705 days ago
- The objective of this activity is to help you understand how to run Velvet in general, how to accurately estimate the insert size of a paired-end library through the use of Bowtie, the primary parameters of velvet, and the process involved in producing a de novo assembly ...
Tags: Bioinformatics, Analysis, Assembly, Genome, Velvet, NGS, Tutorial
2715 days ago
- PRISM is a software for split read (reads which span across a structrual variant -- SV ) mapping and SV calling from the mapping result. PRISM is able to detect small insertions and abitrary size deletions, inversions and tandom duplications with the direction of discordant read pairs. PRISM_CTX ...
Tags: Bioinformatics, Comparative genomics, Genomics, Structure Variation, SV, NGS
2713 days ago
- The automated reconstruction of genome sequences in ancient genome analysis is a multifaceted process. EAGER encompasses both state-of-the-art tools for each step as well as new complementary tools tailored for ancient DNA data within a single integrated solution in an easily accessible format. ...
Tags: Bioinformatics, Ancient, EAGER, Genome, DNA, Sequence, NGS
2713 days ago
- Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Cutadapt helps with these trimming tasks by finding the adapter or primer sequences in an error-tolerant way. It can also modify and filter reads i...
Tags: Bioinformatics, Analysis, Assembly, NGS, Cutadapt
2709 days ago
Understanding Greedy Algorithms
Learning greedy algo for biologist. https://www.topcoder.com/community/data-science/data-science-tutorials/greedy-is-good/ This webpage is also useful for the same: http://learninglover.com/examples.php?id=59 http://www.cs.rpi.edu/~magdon/ps/conference/super_biokdd.pdf https://ocw.mit....Tags: Bioinformatics, Assembly, Greedy, Genome, NGS
2712 days ago
- caffMatch is a novel scaffolding tool based on Maximum-Weight Matching able to produce high-quality scaffolds from NGS data (reads and contigs). The tool is written in Python 2.7. It also includes a bash script wrapper that calls aligner in case one needs to first map reads to contigs (instead of...
Tags: Bioinformatics, Analysis, Assembly, Genome, NGS, ScaffMatch, Scaffoldings
2710 days ago
BIMA V3: an aligner customized for mate pair library sequencing
Summary: Mate pair library sequencing is an effective and economical method for detecting genomic structural variants and chromosomal abnormalities. Unfortunately, the mapping and alignment of mate pair read pairs to a reference genome is a challenging and time consuming process for most NGS alig...Tags: Bioinformatics, Analysis, Genome, Mapping, NGS, BIMA, Reads
2709 days ago
