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...2320 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...1929 days ago
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...2367 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...2350 days ago
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...1919 days ago
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...2370 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...2329 days ago
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...1549 days ago
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...795 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...2166 days ago