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...2329 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...2321 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/pandaseq2952 days ago
2952 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...1920 days ago
825 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...3920 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...2686 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...2495 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...3780 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...3519 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...3395 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...2037 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 / -...1735 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/...2020 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...416 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...421 days ago