Results for "aligner"
Blogs
BBTools for bioinformatician !
...-------------------------------------- Generate ROC curves from any aligner [*]index the reference...sam file...substitute this command with the appropriate one from your aligner of choice Code: $ bbmap.s...2322 days ago
Software for genome assembly !
...busco.ezlab.org/ 10 Bandage graph assembly viewer https://rrwick.github.io/Bandage/ 11 Gepard dotter http://cube.univie.ac.at/gepard 12 MUMmer aligner and plotter http://mummer.sou...1396 days ago
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Bookmarks
- LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful...
2991 days ago
- ...for high-sensitivity, genome-wide synteny; Papaya, an all-purpose alignment tool for less diverged sequences; and SLAP, a context-sensitive local aligner for diverged sequences with l...
3060 days ago
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Top-level pages
Commercial and public next-gen-seq (NGS) software
...wtie - Ultrafast, memory-efficient short read aligner. It aligns short DNA sequence.... (published in BMC Bioinformatics)Short read aligner called Bowtie (http://bowtie-...es using the ultra high-throughput short read aligner Bowtie, and then analyzes the...3571 days ago
Software packages for next gen sequence analysis
...ry Merriman at UCLA. * Bowtie - Ultrafast, memory-efficient short read aligner. It aligns short DNA sequence...to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the...3294 days ago
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Wire posts
News
Cleaner BLAST Databases for More Accurate Results
...cross-species screening (FCS-GX) detects contamination from foreign organisms in genomes and other sequences using the genome cross-species aligner (GX) Average Nucleotid...64 days ago
Bio-Scripts
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 in paired rea...2176 days ago
Tags
minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences
git clone https://github.com/lh3/minimap2 cd minimap2 && make # long sequences against a reference genome ./minimap2 -a test/MT-human.fa test/MT-orang.fa > test.sam # create an index first and then map ./minimap2 -d MT-human.mmi test/MT-human.fa ./minimap2 -a MT-human.mmi test/MT...Tags: minimap2, versatile, pairwise, aligner, genomic, spliced, nucleotide, sequences
2198 days ago
Glia: a Graph/Smith-Waterman (partial order) aligner/realigner
glia's main use is as a local realigner. It will realign reads to a set of known (or putative) variants in a VCF, both consuming and producing an ordered stream of BAM alignments. More at https://github.com/ekg/glia glia -f ~/human_g1k_v37.fasta -t 20:62900077-62902077 -v variants.vc...Tags: Glia, Graph, Smith-Waterman, partial, order, aligner, realigner
1611 days ago
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Comments
Comment on "Next generation sequencing in R or bioconductor environment"
R package SPP for chip-seq analysis. It can read quite a few aligner's output file. Here is the original package tutorial. http://compbio.med.harvard.edu/Supplements/ChIP-seq/tutorial...3675 days ago
