Results for "Alignment"
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Download and install MUMmer Align your assembly to a reference genome using nucmer (from MUMmer package) $ nucmer -maxmatch -l 100 -c 500 REFERENCE.fa ASSEMBLY.fa -prefix OUT Consult the MUMmer manual if you encounter problems Optional: Gzip the delta file to speed up upload (usually 2-4X f...Tags: assemblytics, delta, analyze, alignment, assembly, reference, genome, visualization
2145 days ago
AlignQC: A tool for assessing an alignment, and generating reports that are easy to share
Long read alignment analysis. Generate a reports on sequence alignments for mappability vs read sizes, error patterns, annotations and rarefraction curve analysis. The most basic analysis only requires a BAM file, and outputs a web browser compatible xhtml to visualize/share/store/extract analysi...Tags: AlignQC, tool, assessing, alignment, reports, easy, share, NGS, reads
2091 days ago
Mulan: Multiple-sequence local alignment and visualization for studying function and evolution
Mulan: Multiple-sequence local alignment and visualization for studying function and evolution Mulan (http://mulan.dcode.org/), a novel method and a network server for comparing multiple draft and finished-quality sequences to identify functional elements conserved over evolutionary time. Mulan ...Tags: Mulan, Multiple-sequence, local, alignment, visualization, study, function, evolution
2074 days ago
Qualimap2: Evaluating next generation sequencing alignment data
Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts. Supported types of experiments i...Tags: Qualimap2, Evaluating, next, generation, sequencing, alignment, coverage, plot, ngs, bam
2056 days ago
rHAT: a seed-and-extension-based noisy long read alignment tool
rHAT is a seed-and-extension-based noisy long read alignment tool. It is suitable for aligning 3rd generation sequencing reads which are in large read length with relatively high error rate, especially Pacbio's Single Molecule Read-time (SMRT) sequencing reads.Tags: rHAT, seed-and-extension-based, noisy, long, read, alignment, tool, ont, pacbio
2044 days ago
MSAProbs - Parallel and accurate multiple sequence alignment
MSAProbs is a well-established state-of-the-art multiple sequence alignment algorithm for protein sequences. The design of MSAProbs is based on a combination of pair hidden Markov models and partition functions to calculate posterior probabilities. Assessed using the popular benchmarks: BAli...Tags: MSAProbs, Parallel, accurate, multiple, sequence, alignment
1754 days ago
Cactus: a reference-free whole-genome multiple alignment program
Cactus is a reference-free whole-genome multiple alignment program. The principal algorithms are described here: https://doi.org/10.1101/gr.123356.111 Cactus uses substantial resources. For primate-sized genomes (3 gigabases each), you should expect Cactus to use approximately 120 CPU-days ...Tags: Cactus, reference-free, whole-genome, multiple, alignment, program
1721 days ago
Kalign: fast multiple sequence alignment program for biological sequences.
Kalign is a fast multiple sequence alignment program for biological sequences. Align sequences and output the alignment in MSF format: kalign -i BB11001.tfa -f msf -o out.msf Align sequences and output the alignment in clustal format: kalign -i BB11001.tfa -f clu -o out.clu Re-align seq...Tags: Kalign, fast, multiple, sequence, alignment, biological, sequences
1640 days ago
Shouji: a fast and efficient pre-alignment filter for sequence alignment
The ability to generate massive amounts of sequencing data continues to overwhelm the processing capacity of existing algorithms and compute infrastructures. In this work, we explore the use of hardware/software co-design and hardware acceleration to significantly reduce the execution time of sho...Tags: Shouji, fast, efficient, pre-alignment, filter, sequence, alignment
1637 days ago
- Variation graphs provide a succinct encoding of the sequences of many genomes. A variation graph (in particular as implemented in vg) is composed of: nodes, which are labeled by sequences and ids edges, which connect two nodes via either of their respective ends paths, describe genomes,...
Tags: VG, variation, graph, structures, interchange, formats, alignment, genotyping, variant, calling, methods, snp
1552 days ago
