Jit
Enthusiast computational biologist with business dream !!!
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SISRS: Site Identification from Short Read Sequences
By Abhimanyu Singh 2189 days agogithub.com - Next-gen sequence data such as Illumina HiSeq reads. Data must be sorted into folders by taxon (e.g. species or genus). Paired reads in fastq format must be specified by _R1 and _R2 in the (otherwise identical) filenames. Paired and unpaired reads...TULIP - The Uncorrected Long read Itegration Pipeline
By Jit 2559 days agogithub.com - #Running TULIP (The Uncorrected Long-read Integration Process), version 0.4 late 2016 (European eel) TULIP currently consists of to Perl scripts, tulipseed.perl and tulipbulb.perl. These are very much intended as prototypes, and additional...SALSA: A tool to scaffold long read assemblies with Hi-C
By Jit 2355 days agogithub.com - This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch. To use the latest version,...rHAT: a seed-and-extension-based noisy long read alignment tool
By Abhimanyu Singh 2255 days agogithub.com - rHAT is a seed-and-extension-based noisy long read alignment tool. It is suitable for aligning 3rd generation sequencing reads which are in large read length with relatively high error rate, especially Pacbio's Single Molecule Read-time (SMRT)...URMAP, an ultra-fast read mapper
By Jit 1487 days ago Comments (1)github.com - URMAP, a new read mapping algorithm. URMAP is an order of magnitude faster than BWA with comparable accuracy on several validation tests. On a Genome in a Bottle (GIAB) variant calling test with 30× coverage 2×150 reads, URMAP achieves...NCBI PSI-BLAST Tutorial
By Jitendra Narayan 4112 days agohttp:--www.biotechnology.jhu.edu- Tutorial for PSI-BLAST, an extension of BLAST that uses matrix algebra. BLAST is a cornerstone bioinformatics tool at NCBI. BLAST is the Basic Local Alignment Search tool and will protein and DNA sequences that are...Sequencing By Xpansion
By Jitendra Narayan 3448 days agoXpandomer in a single drop reaction to sequence an entire human genome 1000X over.methylKit
By Jit 3097 days agogithub.com - methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods such as Agilent...Kaiju
By Jit 3073 days agohttp://kaiju.binf.ku.dk/ - Kaiju is a program for the taxonomic classification of metagenomic high-throughput sequencing reads. Each read is directly assigned to a taxon within the NCBI taxonomy by comparing it to a reference database containing microbial and viral protein...Software and Tools to detect structure variation with long reads !!
By Archana Malhotra 2812 days agoStructural variation caller tools using long reads
