Results for "Pre-Alignment"
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Comment on "Extract fasta sequence from a multifasta file with fasta header Ids"
perl -ne 'if(/^>(\S+)/){$c=grep{/^$1$/}qw(id1 id2)}print if $c' fasta.file If you have a large number of sequences that you want to extract, then you most likely have...2090 days ago
Comment on "HALC: High throughput algorithm for long read error correction"
Inputs Long reads in FASTA format. Contigs assembled from the corresponding short reads in FASTA format. The initial short reads in FASTA format (only for...2271 days ago
Comment on "Nanopolis: polish a genome assembly"
# Index the draft genome bwa index draft.fa # Align the basecalled reads to the draft sequence bwa mem -x ont2d -t 8 draft.fa reads.fa | samtools sort -o reads.sorted...2279 days ago
Comment on "Installing Perl environment on Linux"
curl -L http://cpanmin.us | perl - --sudo App::cpanminus The above is installing the "zero configuration CPAN modules installer" called cpanm. (Can take several minutes to install - don't break the process) and after - simply: cpanm Foo cpanm Module::One cpanm Another::Module2306 days ago
Comment on "Run miniasm assembler on nanopore reads !"
Here’s the quick and dirty of what was done: 1 Run minimap: This uses a pre-built set of defaults (the ava-pb in the code below) for analyzing PacBio dat...2347 days ago
Comment on "poRe: an R package for the visualization and analysis of nanopore sequencing data"
We now need to install the poRe dependencies in R, which is very easy: R source("http://www.bioconductor.org/biocLite.R") biocLite("rhdf5") install.package...2354 days ago
Comment on "SPAdes hybrid genome assembly"
use SPAdes to assemble the data. SPAdes is a swiss-army knife of genome assembly tools, and by default includes read correction. This takes up lots of RA...2354 days ago
- Canu is one of the best de novo assemblers available for long reads - it’s a fork and updated version of the Celera assembler that was used to assemble the huma...
2355 days ago
Comment on "Run miniasm assembler on nanopore reads !"
I followed this to assemble the genome using ONT (nanopore reads) Minimap and miniasm are ultrafast tools for (i) mapping and (ii) assembly. Designed for long, noisy read...2355 days ago
Comment on "Perl one-liner for bioinformatician !!!"
Convert file to lowercase dd $ dd if=input.txt of=output.txt conv=lcase tr $ tr '[:upper:]' '[:lower:]' < input.txt > output.txt awk $ awk '{ print tolower($0...2394 days ago
