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flexidot: Highly customizable, ambiguity-aware dotplots for visual sequence analyses
By Jit 1703 days agogithub.com - FlexiDot is a cross-platform dotplot suite generating high quality self, pairwise and all-against-all visualizations. To improve dotplot suitability for comparison of consensus and error-prone sequences, FlexiDot harbors routines for strict and...AfterQC: Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
By Jit 2368 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...SeqMonk:A tool to visualise and analyse high throughput mapped sequence data
By Jit 2294 days agowww.bioinformatics.babraham.ac.uk - SeqMonk is a program to enable the visualisation and analysis of mapped sequence data. It was written for use with mapped next generation sequence data but can in theory be used for any dataset which can be expressed as a series of genomic...NanoPack: visualizing and processing long-read sequencing data
By Jit 2189 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 compatible...ClinCNV: Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data
By Neel 1802 days agogithub.com - ClinCNV detects CNVs in germline and somatic context in NGS data (targeted and whole-genome). We work in cohorts, so it makes sense to try ClinCNV if you have more than 10 samples (recommended amount - 40 since we estimate variances from...Submit your SARS-CoV-2 sequence data to GenBank
By Neel 1718 days agoSubmit your SARS-CoV-2 sequence data to GenBank and SRA with our new submission landing page.
Libraries or management tools for high throughput sequencing data
Last updated 79 days ago by LEGEGATB Library. The Genome Analysis Toolbox with de-Bruijn graph. A large part of tools developed by the GenScale team are based on this library.These methods enable the analysis of data sets of any size on multi-core desktop...Understanding Fastqc Output
By Jit 3173 days agowww.bioinformatics.babraham.ac.uk - Understanding Following table and graphs Duplication level kmer profile per base GC content per base N content per base quality per base sequence content per sequence GC content per sequence quality sequence length distribution More at...Samtools Primer !!
By Jit 3104 days agobiobits.org - SAMtools: Primer / Tutorial by Ethan Cerami, Ph.D.keywords: samtools, next-gen, next-generation, sequencing, bowtie, sam, bam, primer, tutorial, how-to, introductionRevisions 1.0: May 30, 2013: First public release on...Maq: Mapping and Assembly with Quality
By Jit 2952 days agomaq.sourceforge.net - Maq stands for Mapping and Assembly with Quality It builds assembly by mapping short reads to reference sequences. Maq is a project hosted by SourceForge.net. The project page is available athttp://sourceforge.net/projects/maq/....
