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Wtdbg2: a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore
By Neel 2907 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 output. Wtdbg2...TULIP - The Uncorrected Long read Itegration Pipeline
By Jit 3237 days agogithub.com - #Running TULIP (The Uncorrected Long-read Integration Process), version 0.4 late 2016 (European eel) TULIP currently consists of to Perl scripts, tulipseed.perl and tulipbulb.perl. These are very much intended as prototypes, and additional...TULIP - The Uncorrected Long read Integration Pipeline
By Jit 3064 days agogithub.com - TULIP currently consists of two Perl scripts, tulipseed.perl and tulipbulb.perl. These are very much intended as prototypes, and additional components and/or implementations are likely to follow. Tulipseed takes as input alignments files of long...SimLoRD: A read simulator for third generation sequencing reads
By Aaryan Lokwani 2965 days agobitbucket.org - SimLoRD is a read simulator for third generation sequencing reads and is currently focused on the Pacific Biosciences SMRT error model. Reads are simulated from both strands of a provided or randomly generated reference sequence. The reference...Metabuli 분리 improves metagenomic read classification
By Abhi 1218 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...BlasR Mapping single molecule sequencing reads using Basic Local Alignment with Successive...
By Jit 3056 days agobix.ucsd.edu - BLASR (Basic Local Alignment with Successive Refinement) for mapping Single Molecule Sequencing (SMS) reads that are thousands to tens of thousands of bases long with divergence between the read and genome dominated by insertion and deletion...Mugsy: multiple whole genome alignment tool
By Jit 3221 days ago Comments (1)mugsy.sourceforge.net - Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for pairwise alignment, a custom graph based segmentation procedure for identifying collinear regions, and the segment-based progressive multiple alignment strategy from Seqan::TCoffee....UniAligner: a parameter-free framework for fast sequence alignment
By Abhi 939 days agogithub.com - UniAligner (formerly, TandemAligner) is the first parameter-free algorithm for sequence alignment that introduces a sequence-dependent alignment scoring that automatically changes for any pair of compared sequences. Classical alignment approaches,...poRe: an R package for the visualization and analysis of nanopore sequencing data
By Jit 3237 days ago Comments (1)academic.oup.com - Motivation: The Oxford Nanopore MinION device represents a unique sequencing technology. As a mobile sequencing device powered by the USB port of a laptop, the MinION has huge potential applications. To enable these applications, the...GPOPSIM: a simulation tool for whole-genome genetic data
By Jit 3182 days agogithub.com - GPOPSIM is a simulation tool for pedigree, phenotypes, and genomic data, with a variety of population and genome structures and trait genetic architectures. It provides flexible parameter settings for a wide discipline of users, especially can...
