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HTSlib
By Jit 2811 days agohttp://www.htslib.org/ - Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories: SamtoolsReading/writing/editing/indexing/viewing SAM/BAM/CRAM formatBCFtoolsReading/writing BCF2/VCF/gVCF files and...Fools guide
By Poonam Mahapatra 2793 days agosfg.stanford.edu - This website and accompaning documents are intended as a tool to help researchers dealing with non-model organisms acquire and process transcriptomic high-throughput sequencing data without having to learn extensive bioinformatics skills. It covers...CABOG: Celera Assembler with Best Overlap Graph
By Abhimanyu Singh 2750 days agowww.jcvi.org - CABOG (Celera Assembler with Best Overlap Graph) is scientific software for DNA research. CABOG has been a critical component of many genome sequencing projects. CABOG operates on small genomes such as bacterial as well as large genomes such as...GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies.
By Abhimanyu Singh 2742 days agogithub.com - GRASS (GeneRic ASsembly Scaffolder)-a novel algorithm for scaffolding second-generation sequencing assemblies capable of using diverse information sources. GRASS offers a mixed-integer programming formulation of the contig scaffolding problem, which...Sr.Bioinformatics Analyst (NGS) at Ocimum
JOB FUNCTIONBio Tech/R&D/Scientist INDUSTRYBiotechnology/Pharmaceutical/Medicine SPECIALIZATIONBasic Research,Bio-Statistician,Clinical Research QUALIFICATION Any Post Graduate BA (Arts), B.Com. (Commerce), BE/ B.Tech (Engineering),...BBTools for bioinformatician !
By Surabhi Chaudhary 2474 days ago Comments (1)BBTools can do almost everything now !Porechop: tool for finding and removing adapters from Oxford Nanopore reads
By Rahul Nayak 2371 days agogithub.com - Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop...RNA-seq Analysis Workshop Course Materials
By Jit 2336 days agochagall.med.cornell.edu - RNAseq can be roughly divided into two "types": Reference genome-based - an assembled genome exists for a species for which an RNAseq experiment is performed. It allows reads to be aligned against the reference genome and significantly improves...nanofilt: Filtering and trimming of long read sequencing data
By Jit 2309 days ago Comments (1)github.com - Filtering on quality and/or read length, and optional trimming after passing filters.Reads from stdin, writes to stdout. Intended to be used: directly after fastq extraction prior to mapping in a stream between extraction and...nQuire: a statistical framework for ploidy estimation using next generation sequencing
By Jit 2243 days agogithub.com - nQuire provides a statistical framework to study organisms with intraspecific variation in ploidy. nQuire is likely to be useful in epidemiological studies of pathogens, artificial selection experiments, and for historical or ancient samples where...
