List of tools frequently used while genome assembly
...10.1) CANU (v. 1.6) Unicycler (v. v0.4.1) Miniasm (v. 0.2-r137-dirty) I have used the following mappers minimap2 (v. 2.0rc1-r232) minimap (v. 0.2-r124-dirty) bwa...1974 days ago
miniasm: very fast OLC-based de novo assembler for noisy long reads
...-vs-all read self-mappings (typically by minimap) as input and outputs an asse...out error correction. It also shows that minimap can be used as a read ov...e useful to produce high-quality assemblies. Minimap and miniasm are ultrafast too...2395 days ago
D-GENIES: A tool for Dotplot large Genomes in an Interactive, Efficient and Simple way
...ine tool designed to compare two genomes. It supports large genome and you can interact with the dot plot to improve the visualisation. We use minimap version 2 to align the two ge...2199 days ago
Alignment-free sequence comparison tools available for next-generation sequencing data analysis
...hs) Software (Python) http://github.com/cbib/MICADo General mapper Minimap Lightweight and fast read ma..., a special type of k-mers) Software (C) https://github.com/lh3/minimap Assembly De novo genome ass...2415 days ago
Run miniasm assembler on nanopore reads !
...-vs-all read self-mappings (typically by minimap) as input and outputs an asse...epeats: fq2fa ONT_A.fastq ONT_A.fasta minimap2 -xava-ont ONT_A.fasta ONT_A....">"$2"\n"$3}' > AONT_miniasm.fasta minimap2 -xasm10 AONT_miniasm.fasta A...2374 days ago
Install miniasm in Linux / Ubuntu
...he following additional packages will be installed: minimap The following NEW packages will be installed: miniasm minimap 0 upgraded, 2 newly installe...p://in.archive.ubuntu.com/ubuntu bionic/universe amd64 minimap amd64 0.2-3 [26.6 kB] Fetche...1594 days ago
Comment on "Run miniasm assembler on nanopore reads !"
minimap2 –x ava-ont \ ../../trimming_practical/nan...anofilt/nanofilt_trimmed.fastq \ | gzip -1 > ./minimap.paf.gz miniasm -f \ ../...ing_practical/nanofilt/nanofilt_trimmed.fastq \ ./minimap.paf.gz > miniasm.gfa &n...840 days ago
Comment on "Run miniasm assembler on nanopore reads !"
...w) for analyzing PacBio data. Minimap only accepts two FASTQ files...single file prior to running minimap. minimap2 -x ava-pb -t 23 \...cat.fastq /home/data/20170911_minimap2_pacbio_oly.paf > /home/da....fastq \ 20170918_oly_pacbio_minimap_mappings.paf \ 20170918_oly_...2211 days ago