Jit
Enthusiast computational biologist with business dream !!!
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INC-Seq: accurate single molecule reads using nanopore sequencing
By Jit 2552 days agogithub.com - INC-Seq reads enabled accurate species-level classification, identification of species at 0.1 % abundance and robust quantification of relative abundances, providing a cheap and effective approach for pathogen detection and microbiome profiling...Ra assembler - a de novo DNA assembler for third generation sequencing data
By biogeek 2522 days agogithub.com - Integration of the Ra assembler - a de novo DNA assembler for third generation sequencing data developed on Faculty of Electrical Engineering and Computing (FER), Ruder Boskovic Institute (RBI) and Genome Institute of Singapore (GIS). Ra is in...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By Jit 2394 days agogithub.com - Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies. The algorithm uses an A-Bruijn graph to find the overlaps between reads and does not require them to be error-corrected. After...BlasR Mapping single molecule sequencing reads using Basic Local Alignment with Successive...
By Jit 2375 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...ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole...
By Rahul Nayak 2334 days agogithub.com - ChopStitch is a new method for finding putative exons and constructing splice graphs using an assembled transcriptome and whole genome shotgun sequencing (WGSS) data. ChopStitch identifies exon-exon boundaries in de novo assembled RNA-seq data with...NanoPack: visualizing and processing long-read sequencing data
By Jit 2296 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 2255 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)...sim3C: Read-pair simulation of 3C-based sequencing methodologies (HiC, Meta3C, DNase-HiC)
By Jit 2201 days agogithub.com - Required python modules biopython intervaltree numpy scipy tqdm PyYAMLjackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator
By Abhimanyu Singh 1946 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...DeepVariant : an analysis pipeline that uses a deep neural network to call genetic variants from...
By Jit 1763 days agogithub.com - DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation...
