Results for "SPAdes"
Blogs
Bioinformatics tools developed for Oxford Nanopore data analysis !
...ac/ra-integrate/ ALLPATHS-LGde Bruijn graph ALLPATHS-L correctorhttps://www.broadinstitute.org/software/allpaths-lg/blog/?page_id=12 SPAdes de Bruijn graph SPAdes correctorhttp://bioinf.spbau....2500 days ago
List of tools frequently used while genome assembly
List of tools frequently used while genome assembly: I have used the following assemblers Spades (v. 3.10.1) CANU (v. 1.6) Unicycler (v. v0.4.1) Miniasm (v....2109 days ago
- +2 more Blogs
Bookmarks
shovill: Assemble bacterial isolate genomes from Illumina paired-end reads
Shovill is a pipeline which uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other a...1398 days ago
- SPAdes – St. Petersburg genome assembler – is...blies. This manual will help you to install and run SPAdes. SPAdes version 3.7.1 was rel...nd can be downloaded from http://bioinf.spbau.ru/en/spades. Manual at http://spades.bio...
3117 days ago
- +7 more Bookmarks
Files
Evaluation of genome assembly software based on long reads
...re. The 11 software that have been evaluated are: Celera Assembler , Falcon , Miniasm, Newbler , SGA Assembler, Smartdenovo, Abruijn, Ra, DBG2OLC, Spades and Cerulean. The first 8 sof...2099 days ago
- SPAdes—St. Petersburg genome Assembler—was ori...mic DNA sequencing. With time, the functionality of SPAdes was extended to enable assemb...five different assembly pipelines that comprise the SPAdes package and that are used for...
1004 days ago
Top-level pages
Genome Assembly Tools and Software - PART1 !!
...mbly based approach to detect genomic structural variations from whole-genome high-throughput sequencing datasets. SPAdes 3.6.2 – Single-cell Genome Assembler SPAdes (St. Petersburg genome assemb...2865 days ago
- ...umina and Nanopore data, then SPAdes remains a good option for hybrid assembly - SPAdes was used to produce the ...squo;s group. Again, running spades.py will show you the options:...t> RAM limit for SPAdes in Gb (terminates if exceeded...
2530 days ago
- +5 more Top-level pages
Wire posts
News
SPADes team announce new version SPADes v3.15
New SPAdes 3.15.0.0. announced by the SPADes team This release includes such new features as: - CoronaSPAdes pipeline for the assembly of...llocator mimalloc; - PlasmidSPAdes and bgcSPAdes are now provide...bsp;https://cab.spbu.ru/software/spades/1385 days ago
Bio-Scripts
Palindrome Simulation commands !
...interleavedPE.fasta 3326 cd masurca; ~/Tools/MaSuRCA-3.2.3/bin/masurca sim.conf 3327 ./assemble.sh 3328 cd .. 3329 ~/Tools/SPAdes-3.10.1-Linux/bin/spades.py --careful -1 paired_dat1.f...1915 days ago
- (JitMetaENV) ➜ fastQC_out conda install -c bioconda spades Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists.
1396 days ago
- +3 more Bio-Scripts
Comments
Comment on "Short-read assembly using Spades !"
...number of short sequencing reads. SPAdes (St. Petersburg genome assemb...eps for short-read assembly using SPAdes: Quality control of raw...immomatic or FastQC. Running SPAdes: After quality control, the n...uation of assembly: After running SPAdes, the next step is to evaluate...595 days ago
Comment on "Short-read assembly using Spades !"
SPAdes (St. Petersburg genome assemb...brief overview of how to use SPAdes for short-read assembly: Install SPAdes: SPAdes can be downloaded fro...files for each read. Run SPAdes: To run SPAdes, open the term...ditor or a genome browser. SPAdes also provides several options...600 days ago
- +4 more Comments
