Rahul Agarwal
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LoRMA: A tool for correcting sequencing errors in long reads
By Abhimanyu Singh 2742 days agogite.lirmm.fr - An error correction method that uses long reads only. The method consists of two phases: first, we use an iterative alignment-free correction method based on de Bruijn graphs with increasing length of k-mers, and second, the corrected reads are...Big genomic data on Google Cloud Platform
By Reshma Khatun 4162 days agoAs the cost of DNA sequencing has dropped, the volume of data produced has risen into the petabytes. Google is working with the genomics community to define a standard API for working with big genomic data sets in the cloud. Building on Google Cloud...VariantBam: Filtering and profiling of next-generational sequencing data using region-specific rules
By Rahul Nayak 2714 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...CLUSTER INNOVATION CENTER @ UNIVERSITY OF DELHI
Applications for Pre-selection of candidates under ‘Institutions Mode’ for DST-ISPIRE Faculty in Computational Biology/ Systems Biology/ Bioinformatics Applications are invited for pre-selection of candidates for Ministry of Science and...NanoPack: visualizing and processing long-read sequencing data
By Jit 2631 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...IPython: Interactive notebooks
By Rahul Nayak 4141 days agoThe IPython Notebook is a web-based interactive computational environment where you can combine code execution, text, mathematics, plots and rich media into a single documentFlye: Fast and accurate de novo assembler for single molecule sequencing reads
By BioJoker 2533 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...deepTools
By Martin Jones 4140 days agoUser-friendly tools for the normalization and visualization of deep-sequencing datamosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
By Jit 2308 days agogithub.com - mosdepth can output: per-base depth about 2x as fast samtools depth--about 25 minutes of CPU time for a 30X genome.mean per-window depth given a window size--as would be used for CNV calling.the mean per-region given a BED file of regions.a...NIAB Molecular Biology/Bioinformatics Scientist/RA Openings
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