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....2322 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....1931 days ago
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...1220 days ago
2939 days ago
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...1921 days ago
825 days ago
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...2687 days ago
2352 days ago
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/1207 days ago
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...1737 days ago
1217 days ago
Tags: SPAdes, hybrid, genome, assembly, ONT, Nanopore
2352 days ago
Short-read assembly using Spades !
If we only had Illumina reads, we could also assemble these using the tool Spades. You can try this here, or try it later on your own data. Get data We will use the same Illumina data as we used above: illumina_R1.fastq.gz: the Illumina forward reads illumina_R2.fastq.gz: the Illumina reve...Tags: spades, assembly, short, reads, genome, tools
826 days ago
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...417 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...422 days ago