Bioinformatics tools developed for Oxford Nanopore data analysis !
...://last.cbrc.jp/ LINKSSoftware tool for long read scaffolding https://github.com/warrenlr/LINKS/ marginAlignTools to align nanopore reads to a referencehttps://github.com/benedictpat...2335 days ago
BBTools for bioinformatician !
...umber of symbols indicating a reference match (=) and error rate is t...defined" flag, a copy of each reference sequence will be made represe...either a read will match the reference perfectly, OR its reverse-com...m any aligner [*]index the reference Code: $ bbmap.sh ref=refe...2285 days ago
2174 days ago
Converting a VCF into a FASTA given some reference !
Samtools/BCFtools (Heng Li) provides a Perl script vcfutils.pl which does this, the function vcf2fq (lines 469-528) This script has been modified by...2130 days ago
Understanding reads mapping and flags !
Linear Alignment: An alignment of a read to a single reference sequence that may include insertions...ds can be split in to two or more parts, each part would be mapped to reference(it’s not hard-clip...1851 days ago
Bioinformatics tools for telomere to telomere assembly !
...hie)● PanGenie – algorithm that leverages a pangenome reference built from haplotype-resolved...e high-quality de novo plant genomes (Luca Ermini @ermini_luca) Reference: https://www.pacb.com/blog/y...1006 days ago
Run bash script in Perl program !
...stem( "command arg1 arg2" ); OR system( "command", "arg1", "arg2" ); HELP Here are some useful Perl cheat sheets that can be used as a quick reference guide.-- https://www.pcw...651 days ago
Illumina based assembly pipeline steps !
...De novo assembly Primer trimming (Cutadapt; amplicon data only) Choice of multiple assembly tools (SPAdes || Unicycler || minia) Blast to reference genome (blastn) Contiguate a...891 days ago
Common steps for reads mapping !
...Mapping reads to a reference genome is an essential step i...esearch question. Index the reference genome: Before mapping reads,...olves specifying the input data, reference genome, and output file forma...Overall, mapping reads to a reference genome is a complex process t...437 days ago