Results for "Pacbio"
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MARVEL consists of a set of tools that facilitate the overlapping, patching, correction and assembly of noisy (not so noisy ones as well) long reads. The assembly process can be summarized as follows: overlap patch reads overlap (again) scrubbing assembly graph construction and touring o...Tags: MARVEL, assembler, Assembly, Genome, ONT, Nanopore, PacBio
2193 days ago
minialign: fast and accurate alignment tool for PacBio and Nanopore long reads
Minialign is a little bit fast and moderately accurate nucleotide sequence alignment tool designed for PacBio and Nanopore long reads. It is built on three key algorithms, minimizer-based index of the minimap overlapper, array-based seed chaining, and SIMD-parallel Smith-Waterman-Gotoh extension.Tags: minialign, fast, accurate, alignment, tool, PacBio, Nanopore, long, reads
2173 days ago
pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file
pbalign aligns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5) format. The output Compare HDF5 file will be compatible with Quiver if --forQuiver optio...Tags: pbalign, maps, PacBio, reads, reference, sequences, alignments, BAM, NGS
2173 days ago
HALC: High throughput algorithm for long read error correction
HALC, a high throughput algorithm for long read error correction. HALC aligns the long reads to short read contigs from the same species with a relatively low identity requirement so that a long read region can be aligned to at least one contig region, including its true genome region’s repeats i...Tags: HALC, algorithm, long, read, error, correction, NGS, PacBio, Nanopore
2158 days ago
Hercules: a profile HMM-based hybrid error correction algorithm for long reads
Choosing whether to use second or third generation sequencing platforms can lead to trade-offs between accuracy and read length. Several studies require long and accurate reads including de novo assembly, fusion and structural variation detection. In such cases researchers often combine both tech...Tags: Hercules, profile, HMM-based, hybrid, error, correction, algorithm, long, reads, PacBio
2085 days ago
LoRMA: A tool for correcting sequencing errors in long reads
An error correction method that uses long reads only. The method consists of two phases: first, we use an iterative alignment-free correction method based on de Bruijn graphs with increasing length of k-mers, and second, the corrected reads are further polished using long-distance dependenci...Tags: LoRMA, tool, correction, sequencing, errors, long, reads, PacBio, SMRT
2068 days ago
LSC: Improving PacBio Long Read Accuracy by Short Read Alignment
Added Command line argument support. Multi-stage execution modes. Support for parallelization. Now execution proceeds in batches of long reads the size of which can be set by --long_read_batch_size N. Better compressed intermediate files. Added utilities folder. Added support for multiple ...Tags: LSC, Improve, correct, PacBio, Long, Read, Accuracy, Short, Read, Alignment
2068 days ago
Wtdbg2: a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore
Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb&n...Tags: Wtdbg2, de novo, sequence, assembler, long, noisy, reads, PacBio, Oxford, Nanopore, ONT
2025 days ago
Pacasus: Correction of palindromes in long reads from PacBio and Nanopore
Tool for detecting and cleaning PacBio / Nanopore long reads after whole genome amplification. Check the poster from the Revolutionizing Next-Generation Sequencing (2nd edition) conference in the source folder: https://github.com/swarris/Pacasus/blob/master/vib2017.pdf. The prepint version ...Tags: Pacasus, Correction, palindromes, long, reads, PacBio, Nanopore, ngs
2001 days ago
FLAS: fast and high throughput algorithm for PacBio long read self-correction.
FLAS, a wrapper algorithm of MECAT, to achieve high throughput long read self-correction while keeping MECAT's fast speed. FLAS finds additional alignments from MECAT prealigned long reads to improve the correction throughput, and removes misalignments for accuracy.Tags: FLAS, fast, high, throughput, algorithm, PacBio, long read, self-correction
1779 days ago
