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BlasR Mapping single molecule sequencing reads using Basic Local Alignment with Successive...
By Jit 2376 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...nanofilt: Filtering and trimming of long read sequencing data
By Jit 2308 days ago Comments (1)github.com - Filtering on quality and/or read length, and optional trimming after passing filters.Reads from stdin, writes to stdout. Intended to be used: directly after fastq extraction prior to mapping in a stream between extraction and...NanoPack: visualizing and processing long-read sequencing data
By Jit 2297 days agogithub.com - The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are...d2Tools: The toolbox for counting the frequency of k-tuple from sequencing datasets and calculate...
By Jit 2256 days agocode.google.com - d2Tools are the toolbox for counting the frequency of K-tuple from sequencing datasets and then calculating the pairwise dissimilarity matrix between samples with the d2-style(d2/d2*/d2S representing d2/d2Star/d2shepp, respectively)...NanoPack: visualizing and processing long-read sequencing data
By Jit 2160 days agogithub.com - The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are compatible...jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator
By Abhimanyu Singh 1948 days agogithub.com - jackalope simply and efficiently simulates (i) variants from reference genomes and (ii) reads from both Illumina and Pacific Biosciences (PacBio) platforms. It can either read reference genomes from FASTA files or simulate new ones. Genomic variants...FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads
By Jit 1761 days agobioinfo.ut.ee - FastGT is a program package for whole-genome genotyping of genome variants directly from raw sequencing reads. It is written in C and runs in Linux. FastGT uses a list of variant-specific k-mer pairs that are unique in human genome, counts the...FastProNGS: fast preprocessing of next-generation sequencing reads
By Rahul Nayak 1428 days agogithub.com - FastProNGS to integrate the quality control process with automatic adapter removal. Parallel processing was implemented to speed up the process by allocating multiple threads. Compared with similar up-to-date preprocessing tools, FastProNGS is by...
Libraries or management tools for high throughput sequencing data
Last updated 50 days ago by LEGEGATB Library. The Genome Analysis Toolbox with de-Bruijn graph. A large part of tools developed by the GenScale team are based on this library.These methods enable the analysis of data sets of any size on multi-core desktop...FERMI
By Jit 2997 days agogithub.com - Fermi is a de novo assembler with a particular focus on assembling Illumina short sequence reads from a mammal-sized genome. In addition to the role of a typical assembler, fermi also aims to preserve heterozygotes which are...
