String graph based genome assembly software and tools !
...son, the developer of ABySS assembler and Richard Durbin. iii)...ring graph: 1.SGA (String Graph Assembler) https://github.com/jts/...ome assembly. As opposed to most assemblers, which are de Bruijn graph b...m/lh3/fermi/ Fermi is a de novo assembler with a particular focus on as...2371 days ago
Bioinformatics tools developed for Oxford Nanopore data analysis !
...length, which offers great prospects for genome assembly. Generally, assemblers are based on several differe...ttps://sourceforge.net/projects/phusion2/files/smis/ List of assemblers for Oxford Nanopore MinION l...2363 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/pandaseq2994 days ago
2994 days ago
Evaluation of genome assembly software based on long reads
...reference genomes and the results evaluated with the QUAST software. The 11 software that have been evaluated are: Celera Assembler , Falcon , Miniasm, Newbler , SGA Assembler, Smartdenovo, Abruijn, Ra, DB...1963 days ago
867 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...3963 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...2728 days ago
Awesome perl frameworks, libraries and software - PART 2
...interface to the Flickr API hoytech/Thrust - Perl language bindings for Thrust https://github.com/breach/thrust hotwolf/HSW12 - Assembler and IDE for NXP/Freescale/Mot...2537 days ago
Useful Publications and Websites for Deep Sequencing Data Analysis
...enome Research 22:549-556, 2012 Full Text [Describes the String Graph Assembler (SGA), which assembled a huma...Readjoiner: a fast and memory efficient string graph-based sequence assembler. Gonnella & Kurtz, BMC Bi...3822 days ago
Commercial and public next-gen-seq (NGS) software
...mble ABySS - Assembly By Short Sequences. ABySS is a de novo sequence assembler that is designed for very sho...f whole-genome shotgun microreads. ALLPATHS is a whole genome shotgun assembler that can generate high qualit...3562 days ago
Linux operating system aimed at scientists
...was preventing the desktop to not start on VirtualBox has been fixed, the QIIME and Bowtie-Bio tools have been upgraded, the pandaseq paired end assembler has been added, and the begin...3437 days ago
Phased Human Genome Assembly !
...ists of 865 contigs that were assembled with PacBio data generated with the company’s Sequel® System. Using the FALCON-Unzip assembler, maternal and paternal haplot...2079 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 / -...1777 days ago
Installing Platypus on Ubuntu !
..._64-2.7/cython/cwindow.o -L/home/urbe/anaconda3/envs/py27/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/cwindow.so cythoning cython/assembler.pyx to cython/assembler.c /home/urbe/anaconda3/envs/...2062 days ago
Tags: Bioinformatics, NGS, Assembly, Assembler, SPAdes, Reads, Illumina
2981 days ago
CANU: Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing.
Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION). The software is currently alpha level, feel free to use and report issues encountered. Canu is a hierachical assembly pipeline which runs in fo...Tags: Bioinformatics, FASTQ, NGS, Assembly, Genome, CANU, Assembler, Tool, Software
2957 days ago
Comment on "Short-read assembly using Spades !"
...hort-read assembly is the process of constructing a genome sequence from a large number of short sequencing reads. SPAdes (St. Petersburg genome assembler) is a popular software tool f...458 days ago
Comment on "Short-read assembly using Spades !"
SPAdes (St. Petersburg genome assembler) is a popular tool for short-read assembly. It can assemble reads generated from Illumina, IonTorrent, PacBio, and Oxford Na...463 days ago