Rahul Agarwal
I'm a Bioinformatician and Programmer
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mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
By Jit 2456 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...FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads
By Jit 2381 days agobioinfo.ut.ee - FastGT is a program package for whole-genome genotyping of genome variants directly from raw sequencing reads. It is written in C and runs in Linux. FastGT uses a list of variant-specific k-mer pairs that are unique in human genome, counts the...HASLR: a hybrid assembler which uses both second and third generation sequencing reads
By BioStar 2284 days agogithub.com - HASLR, a hybrid assembler which uses both second and third generation sequencing reads to efficiently generate accurate genome assemblies. Our experiments show that HASLR is not only the fastest assembler but also the one with the lowest number of...Ktrim: an extra-fast and accurate adapter- and quality-trimmer for sequencing data
By Jit 2000 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...Useful links to therapy, disease, drug and drug-target network data:
By Jit 2255 days agoUseful resources to therapy, disease, drug and drug-target network dataNCBI Webinar
By Jit 4441 days agoIntroducing 3 NCBI Resources to Navigate Testing for Disease Linked Variants: MedGen, GTR and ClinVar
Best book Titles for Learning Bionformatics
Last updated 4739 days ago by Jitendra Narayan Comments (4)Nothing can add to our intellect more than reading a book. In books, we can experience new things that we would not normally be able to experience. It is proved that books can change our lives and other people’s lives. Reading can make...Detail annotation of genes !
By Jit 2763 days agoftp.ncbi.nih.gov - gene_info recalculated daily--------------------------------------------------------------------------- tab-delimited one line per GeneID Column header line is the first line in the file. Note: subsets of gene_info are available in the...Flanker
By Rahul Nayak 1984 days agogithub.com - Flanker, a Python package which performs alignment-free clustering of gene flanking sequences in a consistent format, allowing investigation of mobile genetic elements (MGEs) without prior knowledge of their structure. Flanker can be...GEnView: A phylogeny based comparative genomics software to analyze the genetic environment of genes
By Abhi 1681 days agogithub.com - A phylogeny based comparative genomics software to analyze the genetic environment of genes. The user can select one or several taxa and provide one or several reference protein(s). Genomes and plasmids (based on user choice) will be downloaded from...
