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Figeno: Tool for plotting sequencing data along genomic coordinates.
By LEGE 626 days agogithub.com - Tool for plotting sequencing data along genomic coordinates. FIGENO is a FIGure GENerator for GENOmics With figeno, you can plot various types of sequencing data along genomic coordinates. Video...AfterQC: Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
By Jit 2898 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...Filtlong: quality filtering tool for long reads
By Radha Agarkar 2214 days agogithub.com - Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the...
Is reference genome necessary for gene expression study in transcriptome sequencing or for variant discovery in genome sequencing?
Rahul Agarwal 4706 days agoMagic-BLAST: a tool for mapping large next-generation RNA or DNA sequencing runs against a whole...
By Jit 3082 days agoncbi.github.io - Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Each alignment optimizes a composite score, taking into account simultaneously the two reads of a pair, and in case of...LoRMA: a tool for correcting sequencing errors in long reads such those produced by Pacific...
By Jit 3642 days agowww.cs.helsinki.fi - LoRMA is a tool for correcting sequencing errors in long reads such those produced by Pacific Biosciences sequencing machines. Publication: L. Salmela, R. Walve, E. Rivals, and E. Ukkonen: Accurate selfcorrection of errors in long reads using de...TelomereHunter
By Jit 3045 days agowww.dkfz.de - TelomereHunter is a tool for estimating telomere content from human whole-genome sequencing data. It is designed to take BAM files from a tumor and a matching control sample as input. However, it is also possible to run TelomereHunter with one input...HASLR: a tool for rapid genome assembly of long sequencing reads
By LEGE 2317 days agogithub.com - HASLR is a tool for rapid genome assembly of long sequencing reads. HASLR is a hybrid tool which means it requires long reads generated by Third Generation Sequencing technologies (such as PacBio or Oxford Nanopore) together with Next Generation...KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
By Jit 2891 days ago Comments (1)github.com - KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts. The following tools are currently available in KAT: hist: Create an histogram of k-mer occurrences from a sequence file. Adds metadata in...FQC Dashboard: Integrates FastQC results into a web-based, interactive, and extensible FASTQ...
By Shruti Paniwala 2033 days agogithub.com - FQC is software that facilitates quality control of FASTQ files by carrying out a QC protocol using FastQC, parsing results, and aggregating quality metrics into an interactive dashboard designed to richly summarize individual sequencing runs. The...
