Comment on "Run miniasm assembler on nanopore reads !"
...911_minimap2_pacbio_oly.paf > /home/data/20170918_oly_pacbio_miniasm_reads.gfa 3 Convert miniasm output...elow. awk '$1 ~/S/ {print ">"$2"\n"$3}' 20170918_oly_pacbio_miniasm_reads.gfa > 20170918_oly_pacbio_...2165 days ago
2172 days ago
Comment on "Run miniasm assembler on nanopore reads !"
...ble the genome using ONT (nanopore reads) Minimap and miniasm are ult...assembly. Designed for long, noisy reads, they do not have a correctio...n: minimap -Sw5 -L100 -m0 -t8 reads.fq reads.fq | gzip -1 > re...how many contigs: grep ">" reads.fa | wc -l...2172 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 fastq2251 days ago
Comment on "GraphMap - A highly sensitive and accurate mapper for long, error-prone reads"
...] -r <reference_file> -d <reads_file> -o <output_sam_pa....gmidxsec is also generated. -d, --reads STR Path to the reads file. -...as finished, in the order of input reads. [false] -B, --batch-mb INT R.... This value can be lowered if the reads are known to be accurate. [80...2289 days ago
2341 days ago
Comment on "Does anyone have Nanopore latest updates?"
92% genome coverage of E. coli, average depth of 3.8x. But from just _43_ reads https://github.com/nickloman/massive-nanopore-silliness http://lab.loman.net/2017/03/09/ultrareads-for-nanopore/2550 days ago
2796 days ago
Comment on "Software packages for next gen sequence analysis"
...ome assembly, a genome map, and high-throughput sequencing paired-end data. It has been succesfully tested on the Arabidopsis genome with Illumina reads and a Whole-Genome Profiling...2906 days ago
Comment on "List of popular bioinformatics software/tools"
Mapping single molecule sequencing reads using Basic Local Alignment with Successive Refinement (BLASR) http://bix.ucsd.edu/projects/blasr/3007 days ago