Software and Tools to detect structure variation with long reads !!
...e from split-read alignments, high-mismatch regions, and coverage analysis. Please note the current version of Sniffles requires sorted output from BWA-MEM (use -M and -x parameter)...2596 days ago
Bioinformatics tools developed for Oxford Nanopore data analysis !
...tring graph. List of analysis tools developed for Oxford Nanopore data BWA Fast nanopore data tuned alignment tool https://github.com/lh3/bwa GraphMapMapper for long and...2309 days ago
Nucl2Vec: Local alignment of DNA sequences using Distributed Vector Representation
...ignment.With our new approach we have reduced computation cost forlocal alignment , while achieving accuracy comparable to existingdefacto standard BWA-MEM tool. https://prakharg2...1134 days ago
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Next generation sequencing in R or bioconductor environment
...quickly becoming a universal standard alignment format, and is now supported by a wide variety of alignment tools. Documentation Samtools Website BWA (Burrows-Wheeler Alignment) W...3613 days ago
Commercial and public next-gen-seq (NGS) software
...Written by Ben Langmead and Cole Trapnell. Linux, Windows, and Mac OS X. BWA - Heng Lee's BWT Alignment program - a progression from Maq. BWA is a fast light-weighted tool...3507 days ago
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Mapping with BWA-mem or BWA-sampe in one go with python script !
...T provides a script (https://github.com/ksahlin/BESST/blob/master/scripts/reads_to_ctg_map.py) for obtaining sorted and indexed BAM files with BWA-mem or BWA-sampe in one go. An example c...2112 days ago
Long reads mapper bash script !
...minimap2Loc=/home/urbe/Tools/minimap2-2.3_x64-linux/minimap2 bwaMemLoc=/home/urbe/anaconda3/bin/bwa ngmlrLoc=/home/urbe/Tools/ng...mapping $fileName, present at $refFasta" if [ $toolName == "bwa" ]; then echo "Mapping wi...2111 days ago
Latest paper on comparison of mapping tools
A. Hatem, D. Bozdag, A. E. Toland, U. V. Catalyurek "Benchmarking short sequence mapping tools" BMC Bioinformatics, 14(1):184, 2013. http://bmi.osu.edu/hpc/software/benchmark/ http://bmi.osu.edu/hpc/software/pmap/pmap.html Other similiar papers: http://online.liebertpub.com/doi/pdf/10.1089/cm...Tags: Sequencing, short reads mapping, SNP, GSNAP, BWA, Bowtie, BWA, mrsFAST
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Tags: bwa, mapping, genome, vcf, align, genome
825 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 re...2088 days ago
Comment on "Alignment of closely related whole genomes/scaffolds"
...: fast multiple alignment of closely related whole genomes http://bioinformatics.oxfordjournals.org/content/27/3/334 In my works, I have also used BWA-SW, BLAT and LASTZ. However,...3007 days ago