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...2326 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...2318 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/pandaseq2948 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...
2948 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...1917 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...
821 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...3917 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...2683 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...2491 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...3777 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...3516 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...3391 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...2033 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 / -...1732 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/...2016 days ago
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Tags
Run miniasm assembler on nanopore reads !
Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream assemblers, miniasm does not have a consensus step. I...Tags: Run, miniasm, assembler, nanopore, reads
2327 days ago
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...413 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...418 days ago
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