Next Generation Sequencing (NGS)
https://en.wikipedia.org/wiki/Sequencing
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VariantBam: Filtering and profiling of next-generational sequencing data using region-specific rules
By Rahul Nayak 2271 days agogithub.com - VariantBam is a tool to extract/count specific sets of sequencing reads from next-generational sequencing files. To save money, disk space and I/O, one may not want to store an entire BAM on disk. In many cases, it would be more efficient to store...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...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By BioJoker 2091 days agogithub.com - Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The...ngs-bits - Short-read sequencing tools
By Neel 1802 days agogithub.com - Binaries of ngs-bits are available via Bioconda. Alternatively, ngs-bits can be built from sources: Binaries for Linux/macOS From sources for Linux/macOS From sources for WindowsHASLR: a tool for rapid genome assembly of long sequencing reads
By LEGE 1787 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...Parliament2: Runs a combination of tools to generate structural variant calls on whole-genome...
By Jit 1669 days agogithub.com - Parliament2 identifies structural variants in a given sample relative to a reference genome. These structural variants cover large deletion events that are called as Deletions of a region, Insertions of a sequence into a region, Duplications of a...Smudgeplot: Inference of ploidy and heterozygosity structure using whole genome sequencing data
By Neel 1031 days agogithub.com - This tool extracts heterozygous kmer pairs from kmer count databases and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovB / (CovA +...RePS: Repeat-masked Phrap with scaffolding, a WGS sequence assembler
By Jit 1815 days agoftp.genomics.org.cn - RePS (Repeat-masked Phrap with scaffolding), a WGS sequence assembler, that explicitly identifies exact kmer repeats from the shotgun data and removes them prior to the assembly. The established software Phrap is used to compute meaningful error...Essentials of Statistics and Data Analysis using R
Clinical Development Services Agency (CDSA) is an extramural unit of Translational Health Science and Technology Institute (THSTI), Department of Biotechnology, Ministry of Science & Technology, Government of India. CDSA has a national mandate...SeqMule: Automated human exome/genome variants detection
By BioStar 1770 days agodoc-openbio.readthedocs.io - SeqMule takes single-end or paird-end FASTQ or BAM files, generates a script consisting of more than 10 popular alignment, analysis tools and runs the script line by line. Users can change the pipeline or fine-tune the parameters by modifying its...
