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...3002 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....2356 days ago
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...2978 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...2978 days ago
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...2713 days ago
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...3807 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...3771 days ago
2103 days ago
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.1595 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...2320 days ago