Software and Tools to detect structure variation with long reads !!
Uncovering the connection between genetics and heritable diseases requires an approach that looks at all the variant bases and types in a genome. While a PacBio de...2605 days ago
Bioinformatics tools developed for Oxford Nanopore data analysis !
MinION is the only portable real-time device for DNA and RNA sequencing. Each consumable flow cell can now generate 10–20 Gb of DNA sequence data. U...2318 days ago
Nucl2Vec: Local alignment of DNA sequences using Distributed Vector Representation
We demonstrate a novel approach forlocal alignment of DNA reads with respect to reference genome.For this process we have used Skip-gram model for creatingencoding(Nucl2...1144 days ago
Next Generation Sequencing (NGS) Tutorials
Institute of computational biomedicine, Cornell University provide an NGS workshop tutorial at http://chagall.med.cornell.edu/NGScourse/ You can also add you...3485 days ago
2149 days ago
List of bioinformatics open source projects/software.
Open source software is software that can be freely used, changed, and shared (in modified or unmodified form) by anyone. Open source software is made by many people, an...3754 days ago
Next generation sequencing in R or bioconductor environment
There are many R software and bioconductor packages for NGS data analysis, some of them are as follows Biostrings The Biostrings package from Bioconductor provides an...3622 days ago
3544 days ago
Webinar on Fast and Accurate DNA Variant Calling on 26 Apr 2017
Continuing our DNA-Seq webinar series, we'll present Strand NGS v3.0 best-practices: a workflow that identifies highly accurate variants from raw reads. Our best pr...2569 days ago
3163 days ago
Mapping with BWA-mem or BWA-sampe in one go with python script !
BAM files and mapping BESST requires sorted and indexed BAM files as input. Any read aligner + samtools can be used to obtain such files. Read pairs needs to be aligned...2121 days ago
Long reads mapper bash script !
#!/bin/bash #only for LONG READS mapping #USAGE: runMapper.sh minimap2 ref.fa reads.fa/fq 48 ont echo -e "This is a bash scrip to map your long reads and make it v...2120 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.sort...2097 days ago
Comment on "Alignment of closely related whole genomes/scaffolds"
Hmmm great link Rahul, You can also try Mugsy: fast multiple alignment of closely related whole genomes http://bioinformatics.oxfordjournals.org/content/27/3/334 In my...3016 days ago