www.healthcare.uiowa.edu - Long read alignment analysis. Generate a reports on sequence alignments for mappability vs read sizes, error patterns, annotations and rarefraction curve analysis. The most basic analysis only requires a BAM file, and outputs a web browser...
github.com - rHAT is a seed-and-extension-based noisy long read alignment tool. It is suitable for aligning 3rd generation sequencing reads which are in large read length with relatively high error rate, especially Pacbio's Single Molecule Read-time (SMRT)...
www.bioinformatics.nl - Caretta – a multiple protein structure alignment and feature extraction suite
Caretta, a multiple structure alignment suite meant for homologous but sequentially divergent protein families which consistently returns accurate alignments...
github.com - odgi provides an efficient and succinct dynamic DNA sequence graph model, as well as a host of algorithms that allow the use of such graphs in bioinformatic analyses.
Careful encoding of graph entities allows odgi to efficiently...
github.com - PaReBrick. The tool takes a collection of strains represented as a sequence of oriented synteny blocks and a phylogenetic tree as input data. It identifies rearrangements, tests them for consistency with a tree, and sorts the events by their...
How to download FASTA sequence for certain gene features while in the NCBI's Sequence Viewer.
Sequence Viewer homepage:
www.ncbi.nlm.nih.gov/projects/sviewer/
Sequence Viewer playlist:
https://www.youtube.com/playlist?list=PL76D7EE6A6A8AC1C3
platanus.bio.titech.ac.jp - Platanus is a novel de novo sequence assembler that can reconstruct genomic sequences of highly heterozygous diploids from massively parallel shotgun sequencing data.
The latest version is 1.2.4.
To cite Platanus, please use the...
biobits.org - SAMtools: Primer / Tutorial by Ethan Cerami, Ph.D.keywords: samtools, next-gen, next-generation, sequencing, bowtie, sam, bam, primer, tutorial, how-to, introductionRevisions 1.0: May 30, 2013: First public release on...
The genome assemblers generally take a file of short sequence reads and a file of quality-value as the input. Since the quality-value file for the high throughput short reads is usually highly memory-intensive, only a few assemblers, best suited for...
www.ncbi.nlm.nih.gov - Sequence - Evolution - Function is an introduction to the computational approaches that play a critical role in the emerging new branch of biology known as functional genomics. The book provides the reader with an understanding of the...