Results for "Fragment"
Blogs
Computer simulation of genetic mechanism !!
...://www.ebi.ac.uk/projects/bargen FIGG FIGG is a genome simulation tool that uses known or theorized variation frequency, per a given fragment size and grouped by GC conten...2988 days ago
String graph based genome assembly software and tools !
...o represent all the information in raw reads. If you want to learn about String Graph assembler, please read the following papers - i) The Fragment Assembly String Graph - E. W....2342 days ago
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Bookmarks
PEAR: a fast and accurate Illumina Paired-End reAd mergeR
...and can run with as low as just a few kilobytes of memory. PEAR evaluates all possible paired-end read overlaps and without requiring the target fragment size as input. In addition, i...2964 days ago
REAPR: a universal tool for genome assembly evaluation
...The software requires as input an assembly in FASTA format and paired reads mapped to the assembly in a BAM file. Mapping information such as the fragment coverage and insert size dist...2964 days ago
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Pages
Genome Assembly Tools and Software - PART2 !!
...by NGS and assemblers into longer chromosomal fragments using comparative genome inf...ls from the latest 250 base Illumina PCR-free fragment reads. SeqCons 1.0 – d...mputer program that uses a short starting DNA fragment, often a EST or partial gene...2699 days ago
Top-level pages
Useful Publications and Websites for Deep Sequencing Data Analysis
...cript expression profiling. Łabaj et al, Bioinformatics 27:i383 - i391, 2011 Full Text Improving RNA-Seq expression estimates by correcting for fragment bias. Roberts et al, Genome B...3792 days ago
List of In-silico Binding Site Prediction Tools
...we utilize the Smith-Waterman algorithm to footprint an unbound pocket fragment with those selected from the...uchicago.edu/). The pairwise alignment of the unbound and split-pocket fragments is superimposed to evaluate...3757 days ago
- +3 more Top-level pages
Bio-Scripts
- ...s (BETA Tool) Collects reference and alternate allele counts at specified sites CollectFragmentCounts (BETA Tool) Collects fragment counts at specified intervals...
2088 days ago
Tags
- RapClust is a tool for clustering contigs from de novo transcriptome assemblies. RapClust is designed to be run downstream of the Sailfish or Salmon tools for rapid transcript-level quantification. Specifically, RapClust relies on the fragment equivalence classe...
Tags: RapClust, Accurate, Lightweight, Clustering, de novo, Transcriptomes, Fragment, Equivalence, Classes
2053 days ago
Comments
Comment on "RGFA: powerful and convenient handling of assembly graphs"
The Graphical Fragment Assembly (GFA) is a proposed format which allow to describe the product of sequence assembly. This gem implements the proposed specifications for the GFA format described under https://github.com/GFA-spec/GFA-spec/blob/master/GFA-spec.md as close as possible.1580 days ago
Comment on "GraphMap - A highly sensitive and accurate mapper for long, error-prone reads"
...Determines the format automatically from file extension. fastq - Loads FASTQ or FASTA files. fasta - Loads FASTQ or FASTA files. gfa - Graphical Fragment Assembly format. sam - Sequen...2305 days ago
