String graph based genome assembly software and tools !
..., the developer of ABySS assembler and Richard Durbin. iii)...g graph: 1.SGA (String Graph Assembler) https://github.com/jts/...assembly. As opposed to most assemblers, which are de Bruijn graph b...h3/fermi/ Fermi is a de novo assembler with a particular focus on as...2345 days ago
Bioinformatics tools developed for Oxford Nanopore data analysis !
MinION is the only portable real-time device for DNA and...rs great prospects for genome assembly. Generally, assemblers are based on several differe...net/projects/phusion2/files/smis/ List of assemblers for Oxford Nanopore MinION l...2337 days ago
PAired-eND Assembler for DNA sequences
PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence. More at https://github.com/neufeld/pandaseq2967 days ago
2967 days ago
Evaluation of genome assembly software based on long reads
TGS technologies have been used to produce highly accurate de novo assemb...UAST software. The 11 software that have been evaluated are: Celera Assembler , Falcon , Miniasm, Newbler , SGA Assembler, Smartdenovo, Abruijn, Ra, DB...1936 days ago
840 days ago
Want to Know which genome assembler rule the world ?
Assemblathon 2: evaluating de novo methods of genome assembly http://www.gigasciencejournal.com/content/2/1/10/abstract http://blogs.nature.com/news/2013/07/geno...3936 days ago
Genome Assembly Tools and Software - PART2 !!
...caffolds generated by NGS and assemblers into longer chromosomal frag...RePS 2.0 – WGS Sequence AssemblerRePS (Repeat-masked Phrap...her with virtually any genome assembler and any NGS read mapper that...Automatically Optimise Velvet Assembler ParametersVelvetOptimiser&nbs...2702 days ago
Awesome perl frameworks, libraries and software - PART 2
licheng/gccfilter - gccfilter is a perl filter to colorize and simplify (or e...indings for Thrust https://github.com/breach/thrust hotwolf/HSW12 - Assembler and IDE for NXP/Freescale/Mot...2510 days ago
Useful Publications and Websites for Deep Sequencing Data Analysis
Global overview papers Next generation quantitative gen...49-556, 2012 Full Text [Describes the String Graph Assembler (SGA), which assembled a huma...t and memory efficient string graph-based sequence assembler. Gonnella & Kurtz, BMC Bi...3796 days ago
Commercial and public next-gen-seq (NGS) software
Integrated solutions CLCbio Genomics Workbench - de novo...ly By Short Sequences. ABySS is a de novo sequence assembler that is designed for very sho...gun microreads. ALLPATHS is a whole genome shotgun assembler that can generate high qualit...3535 days ago
Linux operating system aimed at scientists
The Bio-Linux operating system is based on Ubuntu 14.04 LTS (Trusty Tahr), and the p...ed, the QIIME and Bowtie-Bio tools have been upgraded, the pandaseq paired end assembler has been added, and the begin...3410 days ago
Phased Human Genome Assembly !
The new publicly available assembly (PacBio HG00733) has the fewest gaps of any...with the company’s Sequel® System. Using the FALCON-Unzip assembler, maternal and paternal haplot...2052 days ago
Resume the MIRA assembler run !
mira -r manifest_file Usage: mira [options] manifest_file [manifest_file ...] Options: -c / --cwd= directory Change working directory -r / -...1751 days ago
Installing Platypus on Ubuntu !
(py27) ➜ Tools git:(master) ✗ git clone https://github.com/andyrimmer/Platypu...b -lpython2.7 -o build/lib.linux-x86_64-2.7/cwindow.so cythoning cython/assembler.pyx to cython/assembler.c /home/urbe/anaconda3/envs/...2035 days ago