Jit
Enthusiast computational biologist with business dream !!!
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NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data
By Jit 2981 days agogithub.com - NextSV, a meta SV caller and a computational pipeline to perform SV calling from low coverage long-read sequencing data. NextSV integrates three aligners and three SV callers and generates two integrated call sets (sensitive/stringent) for different...d2Tools: The toolbox for counting the frequency of k-tuple from sequencing datasets and calculate...
By Jit 2936 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)...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By Rahul Nayak 2647 days agogithub.com - Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The...FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads
By Jit 2441 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...HASLR: a hybrid assembler which uses both second and third generation sequencing reads
By BioStar 2344 days agogithub.com - HASLR, a hybrid assembler which uses both second and third generation sequencing reads to efficiently generate accurate genome assemblies. Our experiments show that HASLR is not only the fastest assembler but also the one with the lowest number of...Smudgeplot: Inference of ploidy and heterozygosity structure using whole genome sequencing data
By Neel 1682 days agogithub.com - This tool extracts heterozygous kmer pairs from kmer count databases and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovB / (CovA +...Bioinformatics tools developed for Oxford Nanopore data analysis !
By biogeek 3202 days ago Comments (2)One of the technical advantages of ONT data is the read length, which offers great prospects for genome assembly.minialign: fast and accurate alignment tool for PacBio and Nanopore long reads
By Jit 3055 days agogithub.com - Minialign is a little bit fast and moderately accurate nucleotide sequence alignment tool designed for PacBio and Nanopore long reads. It is built on three key algorithms, minimizer-based index of the minimap overlapper, array-based seed chaining,...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...Nanopore adaptor !
By Jit 2435 days agogithub.com - Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads....
