Results for "minimap2"
Blogs
List of tools frequently used while genome assembly
...Spades (v. 3.10.1) 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) m...1957 days ago
Bookmarks
minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences
...clone https://github.com/lh3/minimap2 cd minimap2 && make # long seque...human.mmi test/MT-human.fa ./minimap2 -a MT-human.mmi test/MT-orang...ord Nanopore genomic reads ./minimap2 -ax sr ref.fa read1.fa read2....d command line options man ./minimap2.12173 days ago
Rebaler: program for conducting reference-based assemblies using long reads.
Rebaler is a program for conducting reference-based assemblies using long reads. It relies mainly on minimap2 for alignment and Racon for making consensus sequences...2083 days ago
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Top-level pages
Run miniasm assembler on nanopore reads !
...the detail of the reads repeats: fq2fa ONT_A.fastq ONT_A.fasta minimap2 -xava-ont ONT_A.fasta ONT_A.f...S' AONT.gfa |awk '{print ">"$2"\n"$3}' > AONT_miniasm.fasta minimap2 -xasm10 AONT_miniasm.fasta AO...2357 days ago
Some useful Bioinformatics links
...ts&serviceurl=https%3A%2F%2Fprojects.zoho.eu%2Fportal%2Favaga2 lh3/minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences https://github.com/lh3/minimap2 SSPACE-LongRead: scaffolding...2269 days ago
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Wire posts
Bio-Scripts
Install Minimap2 using conda !
vik@vik-Lenovo-ideapad-320-15ISK:~/Downloads/setu/setu$ conda install -c bioconda minimap2 Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists.1082 days ago
Long reads mapper bash script !
...S mapping #USAGE: runMapper.sh minimap2 ref.fa reads.fa/fq 48 ont ec...graphmap/bin/Linux-x64/graphmap minimap2Loc=/home/urbe/Tools/minimap2-...echo "#USAGE: runMapper.sh minimap2 ref.fa reads.fa/fq 48 ont"...cbio" fi elif [ $toolName == "minimap2" ]; then echo "Mapping wi...2150 days ago
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Comment on "Run miniasm assembler on nanopore reads !"
minimap2 –x ava-ont \ ../../trimming_practical/nanofilt/nanofilt_trimmed.fastq \ ../../trimming_practical/nanofilt/nanofilt_trimmed.fastq \ | gzip -1 > ./...824 days ago
Comment on "Run miniasm assembler on nanopore reads !"
...into a single file prior to running minimap. minimap2 -x ava-pb -t 23 \ 20170911_o...0170911_oly_pacbio_cat.fastq \ > 20170911_minimap2_pacbio_oly.paf 2 Run miniasm...gs are required for Racon assembly (Step 5). minimap2 \ -t 23 \ 20170918_oly_pacb...2194 days ago
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