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AfterQC: Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
By Jit 2961 days ago Comments (1)github.com - Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data AfterQC can simply go through all fastq files in a folder and then output three folders: good, bad and QC folders, which contains good reads, bad reads and the QC...MITOS: improved de novo metazoan mitochondrial genome annotation
By Jit 2841 days agomitos.bioinf.uni-leipzig.de - Allows automatic annotation of metazoan mitochondrial genomes. MITOS is a pipeline designed to compute a consistent de novo annotation of the mitogenomic sequences. The software allows for a systematic error screening, the standardisation of gene...kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity
By Rahul Nayak 2991 days agogithub.com - The k-mer Weighted Inner Product. This software implements a de novo, alignment free measure of sample genetic dissimilarity which operates upon raw sequencing reads. It is able to calculate the genetic dissimilarity between samples without any...Tallymer: method to compute K-mer frequencies and its application to annotate large repetitive...
By Jit 3094 days agowww.zbh.uni-hamburg.de - Tallymer is based on enhanced suffix arrays. This gives a much larger flexibility concerning the choice of the k-mer size. Tallymer can process large data sizes of several billion bases. We used it in a variety of applications to study the...CheckM:Assessing the quality of microbial genomes recovered from isolates, single cells, and...
By Rahul Nayak 2998 days ago Comments (2)ecogenomics.github.io - CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. It provides robust estimates of genome completeness and contamination by using collocated sets of genes that are ubiquitous...Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data
By Shruti Paniwala 2842 days agowww.well.ox.ac.uk - Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. By using local realignment of reads and local assembly it achieves both high sensitivity and high specificity. Platypus can detect...Variant Calling Resequencing-Based Genome Inference
By Abhi 737 days agoevomics.org - Variant Calling - Resequencing-Based Genome Inference Erik GarrisonUniversity of Tennessee Health Science CenterWorkshop on Genomics - Český KrumlovJanuary 12,...vcfR: a package to manipulate and visualize VCF data in R
By Jit 2842 days agogithub.com - VcfR is an R package intended to allow easy manipulation and visualization of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R a parser function extracts matrices from...VG: variation graph data structures, interchange formats, alignment, genotyping, and variant...
By Jit 2383 days agogithub.com - Variation graphs provide a succinct encoding of the sequences of many genomes. A variation graph (in particular as implemented in vg) is composed of: nodes, which are labeled by sequences and ids edges, which connect two nodes via either of...The new corona variant has 23 mutations in all, which is unusually huge !
By Shruti Paniwala 2053 days agoThe new SARS-CoV-2 version, B.1.1.7, which was first seen in the third week of September in Kent and Greater London, has since spread to other locations in the UK.
