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gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output
By Rahul Nayak 2447 days agogithub.com - gapFinisher is based on the controlled use of a previously published gap filling tool FGAP and works on all standard Linux/UNIX command lines. They compare the performance of gapFinisher against two other published gap filling tools PBJelly and...LoFreq*: A sequence-quality aware, ultra-sensitive variant caller for NGS data
By BioStar 2423 days agocsb5.github.io - LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or...FiNGS: Filters for Next Generation Sequencing
By Neel 2048 days agogithub.com - Key features Filters SNVs from any variant caller to remove false positives Calculates metrics based on BAM files and provides filtering not possible with other tools Fully user-configurable filtering (including which filters to use and their...
Libraries or management tools for high throughput sequencing data
Last updated 733 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...1mb long DNA with Nanopore technology
By Jit 3213 days agoLongest read of 1mb achievements with NanoporeNanoPack: visualizing and processing long-read sequencing data
By Jit 2842 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...Understanding your reads and mapping !
By Neel 2442 days agobioinformatics-core-shared-training.github.io - One of the best tutorial for beginners ... https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2017/Day1/Session4-seqIntro.htmlSOAP2 : Short Oligonucleotide Analysis Package 2
By Poonam Mahapatra 3058 days agosoap.genomics.org.cn - SOAPaligner/soap2 is a member of the SOAP (Short Oligonucleotide Analysis Package). It is an updated version of SOAP software for short oligonucleotide alignment. The new program features in super fast and accurate alignment for huge amounts of...SVbyEye: R Package to visualize alignments between two or multiple DNA sequences
By LEGE 750 days agogithub.com - R Package to visualize alignments between two or multiple DNA sequences includinga number of functionalities to facilitate processing of alignments in PAF format. SVbyEye, an open-source R package to visualize and annotate sequence-to-sequence...chromoMap-An R package for Interactive visualization and mapping of human chromosomes
By Rahul Nayak 3025 days ago Comments (1)An R package for Interactive visualization and mapping of human chromosomes
