Rahul Nayak
A Bioinformatician
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pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file
By Jit 3047 days agogithub.com - 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...Understanding HiFi Reads !
By Rahul Nayak 1646 days agopacb.com - While little public data is available for either of the new synthetic long read approaches, Illumina showed an example comparison earlier this year at the Festival of Genomics & Biodata conference (FoG 2022). In the IGV screenshot...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By BioJoker 2733 days agogithub.com - Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The...COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
By Jit 3216 days agoftp.genomics.org.cn - An efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE...mixtureS: a novel tool for bacterial strain reconstruction from reads
By BioStar 2227 days agowww.cs.ucf.edu - mixtureS that can de novo identify bacterial strains from shotgun reads of a clonal or metagenomic sample, without prior knowledge about the strains and their variations. Tested on 243 simulated datasets and 195 experimental datasets, mixtureS...HGT-Finder: A New Tool for Horizontal Gene Transfer Finding and Application to Aspergillus genomes
By Jit 3174 days agowww.ncbi.nlm.nih.gov - HGT-Finder: (i) can be used for HGT detection in both prokaryotes and eukaryotes, (ii) can report a statistical P value for each gene to indicate how likely it is to be horizontally transferred, and (iii) is fully automated (requires...miniasm: very fast OLC-based de novo assembler for noisy long reads
By Jit 3225 days agogithub.com - Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream...ReMILO: reference assisted misassembly detection algorithm using short and long reads.
By Jit 3004 days agogithub.com - ReMILO, a reference assisted misassembly detection algorithm that uses both short reads and PacBio SMRT long reads. ReMILO aligns the initial short reads to both the contigs and reference genome, and then constructs a novel data structure called...wtdbg2: A fuzzy Bruijn graph approach to long noisy reads assembly
By BioStar 2791 days agogithub.com - 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...HairSplitter: assembling long reads in an unknown number of haplotypes
By BioStar 1389 days agohal.archives-ouvertes.fr - Pros and cons of HairSplitter Limitations of HairSplitter: Not very fast: it re-polishes the whole assembly Limited in the number of haplotypes Strengths of HairSplitter: Very modular, can be used with any assembler Naive: makes no...
