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Comparison of Short Read De Novo Alignment Algorithms
Excellent article to introduce different sequencing methods along with tools for de novo assembly of sequencing reads and their relevant references. Title: Comparison of Short Read De Novo Alignment Algorithms Author: Nikhil Gopal3891 days ago
Next Generation Sequencing (NGS) Tutorials
...s DOI: 10.1093/bioinformatics/btr441 ngs_backbone: a pipeline for read cleaning, mapping and SNP cal...e-exome data http://www.biomedcentral.com/1471-2105/14/S7/S11 DDBJ read annotation pipeline: a cloud...3469 days ago
- "By removing the time-consuming step of read mapping, the authors reported, Sailfish able to provide quantification estimates 20–30 times faster than current methods without loss of accuracy." Tool link: http://www.cs.cmu.edu/~ckingsf/software/sailfish/
3644 days ago
COSMOS, our workflow management system for NGS data
COSMOS, our Python-based management system for implementing large-scale parallel workflows focusing on, but not restricted to, large-scale short-read "NGS" sequencing data is open-ac...3555 days ago
GraphMap - A highly sensitive and accurate mapper for long, error-prone reads
...cing data.It is designed to handle Oxford Nanopore MinION 1d and 2d reads with very high sensitiv...presents a significant improvement over the state-of-the-art for PacBio read mappers. GraphMap was also d...3206 days ago
Scaffolding of a bacterial genome using MinION nanopore sequencing
...ver, most genomes contain repeated DNA elements that are longer than the read lengths achievable with typic...y resolved. A new generation of sequencers offering substantially longer reads is emerging, notably the Pac...3206 days ago
Resolving the complexity of the human genome using single-molecule sequencing
...uman genome in the form of variation of longer and more complex repetitive DNA that can now be largely resolved with the application of this longer-read sequencing technology. ...3202 days ago
- ...including large event detection Pilon requires as input a FASTA file of the genome along with one or more BAM files of reads aligned to the input FASTA file. Pilon uses read alignment analysis to identif...
2990 days ago
- Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-base...
2974 days ago
RNA-Seq De novo Assembly Using Trinity
...equentially to process large volumes of RNA-seq reads. Trinity partitions the sequ...in common). Chrysalis then partitions the full read set among these disjoint grap...Seq data like so: Trinity --seqType fq --left reads_1.fq --right reads_2.fq --CP...2946 days ago
