Abhimanyu Singh
A bioinformatics beginner
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ngs-bits - Short-read sequencing tools
By Neel 1774 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 WindowsHeap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput...
By Jit 2412 days agogithub.com - Heap, that enables robustly sensitive and accurate calling of SNPs, particularly with a low coverage NGS data, which must be aligned to the reference genome sequences in advance. To reduce false positive SNPs, Heap determines genotypes and calls...CNIDARIA: fast, reference-free phylogenomic clustering
By Shruti Paniwala 3084 days agogithub.com - Motivation: Identification of biological specimens is a major requirement for a range of applications. Reference-free methods analyse unprocessed sequencing data without relying on prior knowledge, but these do not scale to arbitrarily large genomes...1mb long DNA with Nanopore technology
By Jit 2533 days agoLongest read of 1mb achievements with NanoporeVariantBam: Filtering and profiling of next-generational sequencing data using region-specific rules
By Rahul Nayak 2244 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 2161 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...MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization
By Jit 1767 days agogithub.com - MitoZ is a Python3-based toolkit which aims to automatically filter pair-end raw data (fastq files), assemble genome, search for mitogenome sequences from the genome assembly result, annotate mitogenome (genbank file as result), and mitogenome...MetaSim A Sequencing Simulator for Genomics and Metagenomics.
By Jit 2548 days agoab.inf.uni-tuebingen.de - Our software can be used to generate collections of synthetic reads that reflect the diverse taxonomical composition of typical metagenome data sets. Based on a database of given genomes, the program allows the user to design a...SimLoRD: A read simulator for third generation sequencing reads
By Aaryan Lokwani 2287 days agobitbucket.org - SimLoRD is a read simulator for third generation sequencing reads and is currently focused on the Pacific Biosciences SMRT error model. Reads are simulated from both strands of a provided or randomly generated reference sequence. The reference...NGS Platforms launched by BGI’s MGI Tech
By Jit 2146 days agoMGI, a subsidiary of global genomics leader BGI Group, announced pricing and its first early access customer for the new ultra high-throughput sequencer, MGISEQ-T7, saying it has driven down sequencing cost to $5 per gigabyte
