Results for "miniasm"
Blogs
Bioinformatics tools developed for Oxford Nanopore data analysis !
...ectorhttps://github.com/marbl/canu FalconString graph, Celera OLC Falcon correctorhttps://github.com/PacificBiosciences/falcon Miniasm OLChttps://github.com/lh3/miniasm ra-integrateOLChttps://githu...2324 days ago
List of tools frequently used while genome assembly
...tly 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. 0.2-r137-dirty) I...1933 days ago
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Unicycler: Hybrid assembly pipeline for bacterial genomes
...sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) where it runs a miniasm+Racon pipeline. For the...2371 days ago
miniasm: very fast OLC-based de novo assembler for noisy long reads
...t from mainstream assemblers, miniasm does not have a consensus ste...the raw input reads. So far miniasm is in early development stage...used, not the whole dataset), miniasm finishes the assembly, includ...rrectors and consensus tools, miniasm may also be useful to produce...2354 days ago
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Files
Evaluation of genome assembly software based on long reads
...4 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, Sma...1923 days ago
Top-level pages
Alignment-free sequence comparison tools available for next-generation sequencing data analysis
...ion technique MinHash Software (Java) https://github.com/marbl/MHAP Miniasm Assembler of long noisy read...correction stage (uses minimap) Software (C) https://github.com/lh3/miniasm LINKS Scaffolding genome as...2374 days ago
Run miniasm assembler on nanopore reads !
Miniasm is a very fast OLC-based de nov...ifferent from mainstream assemblers, miniasm does not have a consensus ste...0000final.eps Assemble with miniasm: miniasm -f ONT_A.fasta AO...{print}}' AONT_miniasm.paf > AONT_miniasm_self.paf minidot -f 5 -m...2333 days ago
Bio-Scripts
Install miniasm in Linux / Ubuntu
...oads/MitoHunter$ sudo apt install miniasm Reading package lists... Don...EW packages will be installed: miniasm minimap 0 upgraded, 2 newly....com/ubuntu bionic/universe amd64 miniasm amd64 0.2+dfsg-2 [29.3 kB] G...p minimap (0.2-3) ... Setting up miniasm (0.2+dfsg-2) ... Processing...1553 days ago
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
2333 days ago
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Comment on "Run miniasm assembler on nanopore reads !"
...fastq \ | gzip -1 > ./minimap.paf.gz miniasm -f \ ../../trimming_practica...nofilt_trimmed.fastq \ ./minimap.paf.gz > miniasm.gfa awk ’/^S...dnadiff ~/course_data/precompiled/chr17.fasta miniasm.fasta...799 days ago
Comment on "Run miniasm assembler on nanopore reads !"
...> 20170911_minimap2_pacbio_oly.paf 2 Run miniasm: This uses your concatenated FASTQ file and the PAF file output from the miniasm step. The code below is taken...5). minimap2 \ -t 23 \ 20170918_oly_pacbio_miniasm_reads.fasta 20170905_minimap2...2170 days ago
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