2122 days ago
2136 days ago
Comment on "Run miniasm assembler on nanopore reads !"
...ng PacBio data. Minimap only accepts two FASTQ files and you need to map your FASTQ file against itself. So, if y...bio_cat.fastq \ 20170911_oly_pacbio_cat.fastq \ > 20170911_minimap2_pac...ngs Using the default settings maps the FASTQ reads back to the contigs (th...2166 days ago
Comment on "poRe: an R package for the visualization and analysis of nanopore sequencing data"
...ack at the Linux command line: R CMD INSTALL poRe_0.16.tar.gz The fastq extraction scripts for poRe a...ady to go. First off, let’s extract the 2D sequence data as FASTQ from the MinION data. N...2173 days ago
Comment on "SPAdes hybrid genome assembly"
...e 3 kmers to save time: ./SPAdes-3.6.2-Linux/bin/spades.py --only-assembler -t 4 -k 21,51,71 -1 SRR2627175_1.fastq.gz -2 SRR2627175_2.fastq.gz --nanopore minion...2173 days ago
2174 days ago
Comment on "Bioinformatics tools developed for Oxford Nanopore data analysis !"
NanoComp: comparing multiple runs NanoStat: statistic summary report of reads or alignments NanoFilt: filtering and trimming of reads NanoLyse: removing contaminant reads (e.g. lambda control DNA) from fastq2252 days ago
Comment on "Run miniasm assembler on nanopore reads !"
...rbe@urbo214b[allONT] minimap2 -xava-ont both.fastq both.fastq -t20 -X > AONT.paf [][M::m...::main] CMD: minimap2 -xava-ont -t20 -X both.fastq both.fastq[M::main] Real time...214b[allONT] ~/Tools/miniasm/miniasm -f both.fastq AONT.paf > AONT.gfa [][M::...2280 days ago
Comment on "GraphMap - A highly sensitive and accurate mapper for long, error-prone reads"
...ons Input/Output options: -r, --ref STR Path to the reference sequence (fastq or fasta). -i, --index STR Pa...ns are: auto - Determines the format automatically from file extension. fastq - Loads FASTQ or FASTA files....2291 days ago
2343 days ago