2194 days ago
Comment on "Run miniasm assembler on nanopore reads !"
...a > 20170918_oly_pacbio_miniasm_reads.fasta 4 Run minimap with default settings Using the default settings maps the FASTQ reads back to the contigs (the PAF file) created in th...2224 days ago
Comment on "SPAdes hybrid genome assembly"
...627175_2.fastq.gz --nanopore minion.pass.2D.fastq -o SPAdes_hybrid & Use samtools to extract the top contig: head -n 1 SPAdes_hybrid/contigs.fasta samtools faidx SPAdes...2231 days ago
2232 days ago
Comment on "Run miniasm assembler on nanopore reads !"
...fast tools for (i) mapping and (ii) assembly. Designed for long, noisy reads, the..., and therefore the resulting assemblies are contiguous (i.e. long) but very nois...> reads.fa And then count how many contigs: grep ">" reads.fa |...2232 days ago
Comment on "Perl Module Installation"
tar zxf Digest-SHA1-2.13.tar.gz cd Digest-SHA1-2.13 perl Makefile.PL make make test make install2295 days ago
Comment on "Important Journals, Blogs and Forums for Bioinformaticians"
...icsclub.blogspot.com BioToolshttp://bio-tools.org Flags and Lollipopshttp://www.ghastlyfop.com/blog/ Macromolecular Modeling Bloghttp://rosettadesigngroup.com/blog/ Nuevo Blog d...2299 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 fastq2310 days ago
Comment on "Run miniasm assembler on nanopore reads !"
...emoved 147 short overlaps[M::asg_cut_tip] cut 24 tips[M::asg_pop_bubble] popped 1 bubbles and trimmed 0 tips[M::main] ===> Step 5: generating unitigs <===[M::main] Version: 0....2338 days ago
Comment on "GraphMap - A highly sensitive and accurate mapper for long, error-prone reads"
...sed for mapping. Output SAM alignments will be in genome space...mbly format. sam - Sequence Alignment/Mapping format. [auto] -...alignment. sggotoh - Gotoh alignment with affine gaps. Semigl...specified, all (secondary) alignments within (-F FLT) will be...2349 days ago