Rahul Nayak
A Bioinformatician
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VariantBam: Filtering and profiling of next-generational sequencing data using region-specific rules
By Rahul Nayak 2241 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 2159 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 Rahul Nayak 1966 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 1772 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 WindowsiSeqQC: a tool for expression-based quality control in RNA sequencing
By BioStar 1741 days agogithub.com - iSeqQC, an expression-based QC tool that detects outliers either produced due to variable laboratory conditions or due to dissimilarity within a phenotypic group. iSeqQC implements various statistical approaches including unsupervised clustering,...Ktrim: an extra-fast and accurate adapter- and quality-trimmer for sequencing data
By Jit 1380 days agogithub.com - Ktrim is written in C++ for GNU Linux/Unix platforms. After uncompressing the source package, you can find an executable file ktrim under bin/ directory compiled using g++ v4.8.5 and linked with libz...Integrated mRNA and microRNA transcriptome analysis in Strand NGS
By Strand 3398 days agoIntegrated mRNA and microRNA transcriptome analysis in Strand NGSNCBI Remap
By Jit 3207 days agowww.ncbi.nlm.nih.gov - NCBI Remap. This tool is conceptually similar to liftOver in that in manages conversions between a pair of genome assemblies but it uses different methods to achieve these mappings. It is also available through a simple web interface or you can use...AnnotationSketch
By Jit 2707 days agogenometools.org - The AnnotationSketch module is a versatile and efficient C-based drawing library for GFF3-compatible genomic annotations. It is included in the GenomeTools distribution. Additionally, bindings to...multiPhATE: bioinformatics pipeline for functional annotation of phage isolates
By Abhimanyu Singh 2018 days agogithub.com - multiple-genome Phage Annotation Toolkit and Evaluator (multiPhATE). multiPhATE is a throughput pipeline driver that invokes an annotation pipeline (PhATE) across a user-specified set of phage genomes. This tool incorporates a de...
