Results for "Fast"
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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
1644 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
1641 days ago
mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
mosdepth can output: per-base depth about 2x as fast samtools depth--about 25 minutes of CPU time for a 30X genome.mean per-window depth given a window size--as would be used for CNV calling.the mean per-region given a BED file of regions.a distribution of proportion of bases covered at or above...Tags: mosdepth, fast, BAM, CRAM, depth, calculation, WGS, exome, target, sequencing
1628 days ago
SeQuiLa-cov: A fast and scalable library for depth of coverage calculations
The Docker image is available at https://hub.docker.com/r/biodatageeks/. Supplementary information on benchmarking procedure as well as test data are publicly accessible at the project documentation site http://biodatageeks.org/sequila/benchmarking/benchmarking.html#depth-of-coverage. A...Tags: SeQuiLa-cov, fast, scalable, library, depth, coverage, calculations
1599 days ago
RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes
RefKA, a reference-based approach for long read genome assembly. This approach relies on breaking up a closely related reference genome into bins, aligning k-mers unique to each bin with PacBio reads, and then assembling each bin in parallel followed by a final bin-stitching step.Tags: RefKA, fast, efficient, long-read, genome, assembly, approach, large, complex, genomes
1462 days ago
RNA-Bloom: a fast and memory-efficient de novo transcript sequence assembler
RNA-Bloom is a fast and memory-efficient de novo transcript sequence assembler. It is designed for the following sequencing data types: single-end/paired-end bulk RNA-seq (strand-specific/agnostic) paired-end single-cell RNA-seq (strand-specific/agnostic) nanopore RNA-seq (PCR...Tags: RNA-Bloom, fast, memory-efficient, de novo, transcript, sequence, assembler
1393 days ago
FastProNGS: fast preprocessing of next-generation sequencing reads
FastProNGS to integrate the quality control process with automatic adapter removal. Parallel processing was implemented to speed up the process by allocating multiple threads. Compared with similar up-to-date preprocessing tools, FastProNGS is by far the fastest.Tags: FastProNGS, fast, preprocessing, next-generation, sequencing, reads
1223 days ago
MMseqs2: ultra fast and sensitive sequence search and clustering suite
MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The software is designed to run on multi...Tags: MMseqs2, ultra, fast, sensitive, sequence, search, clustering, suite
1199 days ago
MMseqs2: ultra fast and sensitive sequence search and clustering suite
MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The software is designed to run on multi...Tags: MMseqs2, ultra, fast, sensitive, sequence, search, clustering, suite, psiblast
939 days ago
- fastv is an ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. It detects microbial sequences from FASTQ data, generates JSON reports and visualizes the result in HTML reports. This tool can be used to detect viral infectious diseases, like COVID-19. This to...
Tags: virus, detect, fast, identification
873 days ago
