Results for "Assembler"
Blogs
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...2313 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...2305 days ago
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Bookmarks
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/pandaseq2936 days ago
- MIRA is a multi-pass DNA sequence data assembler/mapper for whole genome and EST/RNASeq projects. MIRA assemb...e actually putting too much manual work into it. More at http://mira-assembler.sourceforge.net/docs/Definiti...
2936 days ago
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Files
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...1904 days ago
- SPAdes—St. Petersburg genome Assembler—was originally developed for de novo assembly of genome sequencing data produced for cultivated microbial isolates and for single-cel...
809 days ago
Discussion topics
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...3904 days ago
Pages
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...2670 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...2479 days ago
Top-level pages
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...3764 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...3503 days ago
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Wire posts
News
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...3378 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...2020 days ago
Bio-Scripts
Resume the MIRA assembler run !
mira -r manifest_file Usage: mira [options] manifest_file [manifest_file ...] Options: -c / --cwd= directory Change working directory -r / -...1719 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/...2004 days ago
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Tags
- SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. This manual will help you to install and run SPAdes. SPAdes version 3.7.1 was released under GPLv2 on March 8, 2016 and can be downloaded from http://bioinf.spbau...
Tags: Bioinformatics, NGS, Assembly, Assembler, SPAdes, Reads, Illumina
2923 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
2899 days ago
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Comments
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...400 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...405 days ago
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