Neel
Bioinformatics Beginner
Our Sponsors
Related items
CoverM: Read coverage calculator for metagenomics
By Neel 1302 days agogithub.com - CoverM aims to be a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications. CoverM calculates coverage of genomes/MAGs coverm genome (help) or individual...NanoSim: nanopore sequence read simulator based on statistical characterization.
By Jit 2531 days agowww.bcgsc.ca - NanoSim, a fast and scalable read simulator that captures the technology-specific features of ONT data and allows for adjustments upon improvement of nanopore sequencing technology. The first step of NanoSim is read characterization, which provides...HALC: High throughput algorithm for long read error correction
By Jit 2359 days ago Comments (1)github.com - 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...PureCN: copy number calling and SNV classification using targeted short read sequencing
By Jit 2297 days agobioconductor.org - This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with...Shasta long read assembler
By Jit 1774 days ago Comments (1)github.com - The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells. Computational methods used by the Shasta assembler include: Using...Metabuli 분리 improves metagenomic read classification
By Abhi 537 days agogithub.com - Metabuli 분리 improves metagenomic read classification through metamers, DNA-AA k-mers, to be sensitive and specific, recovering 99% and 98% of DNA or AA classifiers. Metabuli is metagenomic classifier that jointly analyze both DNA and amino...Kaiju
By Jit 3070 days agohttp://kaiju.binf.ku.dk/ - Kaiju is a program for the taxonomic classification of metagenomic high-throughput sequencing reads. Each read is directly assigned to a taxon within the NCBI taxonomy by comparing it to a reference database containing microbial and viral protein...Ribbon: Visualizing complex genome alignments and structural variation:
By Jit 2550 days agohttp://genomeribbon.com/ - Ribbon can be used for long reads, short reads, paired-end reads, and assembly/genome alignments. Instructions for each data format are available by clicking on "instructions" in each tab on the right. Local installation: You can install Ribbon...GMcloser: closing gaps in assemblies accurately with a likelihood-based selection of contig or...
By Shruti Paniwala 2356 days agoacademic.oup.com - GMcloser uses likelihood-based classifiers calculated from the alignment statistics between scaffolds, contigs and paired-end reads to correctly assign contigs or long reads to gap regions of scaffolds, thereby achieving accurate and efficient gap...Syri compares alignments between two chromosome-level assemblies and identifies synteny and...
By Shruti Paniwala 905 days agogithub.com - Syri compares alignments between two chromosome-level assemblies and identifies synteny and structural rearrangements.
