Jit
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RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes
By Rahul Nayak 2135 days agogithub.com - 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...HiTE: a fast and accurate dynamic boundary adjustment approach for full-length Transposable...
By LEGE 167 days agogithub.com - HiTE is a Python software that uses a dynamic boundary adjustment approach to detect and annotate full-length Transposable Elements in Genome Assemblies. In comparison to other tools, HiTE demonstrates superior performance in detecting a...odgi: optimized dynamic genome/graph implementation
By Abhimanyu Singh 1494 days agogithub.com - odgi provides an efficient and succinct dynamic DNA sequence graph model, as well as a host of algorithms that allow the use of such graphs in bioinformatic analyses. Careful encoding of graph entities allows odgi to efficiently...GAPPadder: A Sensitive Approach for Closing Gaps on Draft Genomes with Short Sequence Reads
By Jit 2853 days agogithub.com - This software is provided ``as is” without warranty of any kind. In no event shall the author be held responsible for any damage resulting from the use of this software. The program package, including source codes, executables, and this...HapSolo: An optimization approach for removing secondary haplotigs during diploid genome assembly...
By Jit 1763 days agogithub.com - HapSolo, that identifies secondary contigs and defines a primary assembly based on multiple pairwise contig alignment metrics. HapSolo evaluates candidate primary assemblies using BUSCO scores and then distinguishes among candidate assemblies using...AliTV—interactive visualization of whole genome comparisons
By Jit 2977 days agogithub.com - AliTV, which provides interactive visualization of whole genome alignments. AliTV reads multiple whole genome alignments or automatically generates alignments from the provided data. Optional feature annotations and phylo- genetic information are...SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs
By Neel 1902 days agogithub.com - The first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU architectures. SneakySnake greatly (by more than two orders of magnitude) expedites sequence alignment calculation for both short...MUMmer4: A fast and versatile genome alignment system
By Jit 2953 days agomummer4.github.io - MUMmer4, a substantially improved version of MUMmer that addresses genome size constraints by changing the 32-bit suffix tree data structure at the core of MUMmer to a 48-bit suffix array, and that offers improved speed through parallel processing...JBrowse: Embeddable genome browser built completely with JavaScript and HTML5
By Jit 2807 days agogithub.com - JBrowse is a fast, embeddable genome browser built completely with JavaScript and HTML5, with optional run-once data formatting tools written in Perl. Headline Features: Fast, smooth scrolling and zooming. Explore your genome with unparalleled...VCF Compare !
By Rahul Nayak 1507 days agowiki.bits.vib.be - compare two BWA mapping methods with the online hg18-mapped data We first operate a rapid inspection of the different BAM files using samtools flagstat. Illumina provided chr21 read mapping obtained with their GA IIx deep...
