Jit
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DeepVariant : an analysis pipeline that uses a deep neural network to call genetic variants from...
By Jit 2233 days agogithub.com - DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation...McClintock: Meta-pipeline to identify transposable element insertions using next generation...
By BioStar 1958 days agogithub.com - an integrated bioinformatics pipeline for the detection of TE insertions in whole-genome shotgun data, called McClintock (https://github.com/bergmanlab/mcclintock), which automatically runs and standardizes output for multiple TE detection methods....
Libraries or management tools for high throughput sequencing data
Last updated 520 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...mafTools
By Radha Agarkar 3577 days agogithub.com - Bioinformatics tools for dealing with Multiple Alignment Format (MAF) files.sockeye
By Jit 3305 days agowww.bcgsc.ca - This sockeye software uses the Ensembl database project to import sequence and annotation information from several eukaryotic species. A user can additionally import their own custom sequence and annotation data. Individual annotation objects...bedtools
By Jit 3298 days agobedtools.readthedocs.io - Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For...Salzberg lab
We are a computational biology lab that develops novel methods for analysis of DNA and RNA sequences. Our research includes software for aligning and assembling RNA-seq data, whole-genome assembly, and microbiome analysis. We work closely with...-
Awesome perl frameworks, libraries and software - PART 3
Last updated 3166 days ago by Neelfujiwara/perl-queue-q4pg-lite - simple message queue using PostgreSQL. formbuilder/formbuilder - Perl CGI::FormBuilder module for generating, validating, and processing HTML forms fastly/fastly-perl - Fastly perl... LSC: Improving PacBio Long Read Accuracy by Short Read Alignment
By Abhimanyu Singh 2739 days agowww.healthcare.uiowa.edu - Added Command line argument support. Multi-stage execution modes. Support for parallelization. Now execution proceeds in batches of long reads the size of which can be set by --long_read_batch_size N. Better compressed intermediate files. Added...KAST
By Neel 1473 days agogithub.com - Perform Alignment-free k-tuple frequency comparisons from sequences. This can be in the form of two input files (e.g. a reference and a query) or a single file for pairwise comparisons to be made.
