Results for "Analysis"
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Minia is a short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. The output of Minia is a set of contigs. Minia produces results of similar contiguity and accuracy to other de Bruijn assemblers (e.g. Velvet). Download Minia 2.0.7 L...Tags: Bioinformatics, Analysis, Assembly, Genome, Minia, NGS, de Bruijn
2690 days ago
- 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
2690 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
2690 days ago
Standardized velvet assembly report
Requirements: velvet (velveth velvetg should be in your PATH) R (with Sweave) pdflatex (usually part of TeTeX) ggplot2 (from R prompt type install.packages("ggplot2","proto","xtable")) Perl Optional: BLAT or BLAST (to generate alignments against a reference genome). If using BLAT, ad...Tags: Bioinformatics, Analysis, Assembly, Genome, Velvet, standardized-velvet-assembly-report
2689 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
2689 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
2684 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
2685 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
2683 days ago
E-MEM: Efficient computation of Maximal Exact Matches
E-MEM is a C++/OpenMP program designed to efficiently compute MEMs between large genomes. See the README file for instructions on how to use E-MEM. E-MEM source code The source code can be downloaded here. If you use E-MEM, please cite: N. Khiste, L. Ilie, E-MEM: Efficient comp...Tags: Bioinformatics, Analysis, Match, Genome, E-MEM
2683 days ago
- Comparative genomics remains a pivotal strategy to study the evolution of gene organization, and this primacy is reinforced by the growing number of full genome sequences available in public repositories. Despite this growth, bioinformatic tools available to visualize and compare genomes and to i...
Tags: Bioinformatics, Analysis, Synteny, Database, Genomicus
2682 days ago
