Neel
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SDA: Long-read sequence and assembly of segmental duplications
By Jit 2649 days agowww.nature.com - Segmental Duplication Assembler (SDA; https://github.com/mvollger/SDA) constructs graphs in which paralogous sequence variants define the nodes and long-read sequences provide attraction and repulsion edges, enabling the partition and assembly of...Apollo: a sequence annotation editor
By Abhimanyu Singh 2475 days agogenomebiology.biomedcentral.com - The well-established inaccuracy of purely computational methods for annotating genome sequences necessitates an interactive tool to allow biological experts to refine these approximations by viewing and independently evaluating the data supporting...AccessSyRI: finding genomic rearrangements and local sequence differences from whole-genome...
By Jit 2316 days agogithub.com - AccessSyRI: finding genomic rearrangements andlocal sequence differences from whole-genome assemblies SyRI, a pairwise whole-genome comparison tool for chromosome-level assemblies. SyRI starts by finding rearranged regions and then searches for...flexidot: Highly customizable, ambiguity-aware dotplots for visual sequence analyses
By Jit 2234 days agogithub.com - FlexiDot is a cross-platform dotplot suite generating high quality self, pairwise and all-against-all visualizations. To improve dotplot suitability for comparison of consensus and error-prone sequences, FlexiDot harbors routines for strict and...LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data
By Neel 1809 days ago Comments (1)academic.oup.com - 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...ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data
By LEGE 759 days agogithub.com - ContigExtender, was developed to extend contigs, complementing de novo assembly. ContigExtender employs a novel recursive Overlap Layout Candidates (r-OLC) strategy that explores multiple extending paths to achieve longer and highly accurate...COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
By Jit 3104 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...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By BioJoker 2621 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...Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads
By BioStar 2313 days agogithub.com - Rcorrector has an accuracy higher than or comparable to existing methods, including the only other method (SEECER) designed for RNA-seq reads, and is more time and memory efficient. With a 5 GB memory footprint for 100 million reads, it can be run...DADA2: Fast and accurate sample inference from amplicon data with single-nucleotide resolution
By Jit 2033 days agobenjjneb.github.io - The DADA2 tutorial goes through a typical workflow for paired end Illumina Miseq data: raw amplicon sequencing data is processed into the table of exact amplicon sequence variants (ASVs) present in each sample. The DADA2...
