Jit
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HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
By Jit 2389 days agogithub.com - HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to "just work" with excellent speed and accuracy. We found that previously described haplotype assembly methods are specialized for specific read...NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data
By Jit 2305 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...LoRMA: A tool for correcting sequencing errors in long reads
By Abhimanyu Singh 2274 days agogite.lirmm.fr - An error correction method that uses long reads only. The method consists of two phases: first, we use an iterative alignment-free correction method based on de Bruijn graphs with increasing length of k-mers, and second, the corrected reads are...lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data
By BioJoker 2193 days agogithub.com - lordFAST is a sensitive tool for mapping long reads with high error rates. lordFAST is specially designed for aligning reads from PacBio sequencing technology but provides the user the ability to change alignment parameters depending on the reads...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By Rahul Nayak 1972 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 1766 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 1432 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...FSA: Fast Statistical Alignment
By Jit 2852 days agofsa.sourceforge.net - FSA is a probabilistic multiple sequence alignment algorithm which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences. Much as distance-based phylogenetic reconstruction methods like Neighbor-Joining build a...Trelliscope: flexibly visualize large, complex data in great detail from within the R statistical...
By Jit 1773 days agodeltarho.org - Trelliscope provides a way to flexibly visualize large, complex data in great detail from within the R statistical programming environment. Trelliscope is a component in the DeltaRho environment. For those familiar with Trellis...Calculate the significance of the difference between two trends
By BioStar 625 days ago Comments (1)To calculate the significance of the difference between two trends, you can use a statistical test such as a t-test or ANOVA (analysis of variance).
