Results for "pacbio"
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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
1776 days ago
- Call sviper ~$ ./sviper -s short-reads.bam -l long-reads.bam -r ref.fa -c variants.vcf -o polished_variants This will output a polished_variants.vcf file, that contains all the refined variants. Sometimes it is helpful to look at the polished sequence, e.g. with the IGV browser. In...
Tags: SViper, Swipe, Structural, Variants, ONT, PacBio, reads, Illumina
1593 days ago
pbmm2:A minimap2 frontend for PacBio native data formats
pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been...Tags: pbmm2, minimap2, frontend, PacBio, native, data, formats
1535 days ago
How HiFi Reads Different from Traditional PacBio Long Reads ?
Trying to understand HiFi reads, any link could help ...Tags: HiFi, PacBio, Reads, Third, Generation, Sequencing
1223 days ago
AlignGraph2: similar genome-assisted reassembly pipeline for PacBio long reads
AlignGraph2 is the second version of AlignGraph for PacBio long reads. It extends and refines contigs assembled from the long reads with a published genome similar to the sequencing genome. More at https://academic.oup.com/bib/advance-article-abstract/doi/10.1093/bib/bbab022/61467...Tags: AlignGraph2, genome-assisted, reassembly, pipeline, PacBio, long, reads
1145 days ago
LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data
LoReTTA (Long Read Template-Targeted Assembler), a tool designed for performing de novo assembly of long reads generated from viral genomes on the PacBio platform. LoReTTA exploits a reference genome to guide the assembly process, an approach that has been successful with short reads. https://ac...Tags: LoReTTA, user-friendly, tool, assembly, viral, genomes, PacBio, sequence, data
1044 days ago
MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads
MitoHiFi v3.2 is a python pipeline distributed under MIT License ! MitoHiFi was first developed to assemble the mitogenomes for a wide range of species in the Darwin Tree of Life Project (DToL) https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-023-05385-yTags: MitoHiFi, python, pipeline, mitochondrial, genome, assembly, PacBio, fidelity, reads
240 days ago
Pacbio Long Reads Compatible Software and Tools
The following software packages are known to be compatible with PacBio® data, in addition to PacBio's own SMRT® Analysis suite. All packages are believed to be open source or freely available for non-commercial use. See the individual project sites for up-to-date license information. A se...Tags: Bioinformatics, Chromosome, Genome, NGS, Align, LongReads, LR, Reads, Pacbio
2604 days ago
Software and Tools to detect structure variation with long reads !!
Uncovering the connection between genetics and heritable diseases requires an approach that looks at all the variant bases and types in a genome. While a PacBio de novo assembly resolves the most novel SV variants. 8-10X PacBio coverage of single genomes or trios reveals triple the SVs ...Tags: Bioinformatics, LR, Long, Reads, Tools, Software, Pacbio, Genome, DNA, Sequence, NGS, SV, Variation, Structure
2604 days ago
