BOL

CLARK, a method based on a supervised sequence classification using discriminative k-mers. Considering two distinct specific classification problems (see the article for details), namely (1) the taxonomic classification of metagenomic reads to...

This is a scaffold assembler designed for stLFR reads[1]. It uses the link-reads information from stLFR reads to assemble contigs to scaffolds. Here is an illustration of this pipeline:  

Current Protocols in Bioinformatics is a comprehensive source for protocols and reviews in the multidisciplinary field of bioinformatics, including the areas of analyzing expression patterns, pathway analysis, recognizing functional domains,...

The consequences of alterations in the DNA of cancer cells and subsequent vulnerabilities are not fully understood. This project aims to assign a dependency to every cancer cell in a patient which could be exploited to develop new therapies. This...

Chromosomes here https://hgdownload.cse.ucsc.edu/goldenpath/hg38/chromosomes/

NCBI released a set of GATK-specific dbSNP VCF's, with the "chr" attached. Those can be accessed at ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/GATK/.

List of useful biological databases at ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/

List of publically available databases on google server. More at https://software.broadinstitute.org/gatk/download/bundle ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/GATK/. ftp://ftp.broadinstitute.org/bundle/hg38/hg38bundle/

netGO is an R/Shiny package for network-integrated pathway enrichment analysis.netGO provides user-interactive visualization of enrichment analysis results and related networks. Currently, netGO supports analysis for four species...

Install Picard https://github.com/broadinstitute/picard/releases/tag/2.21.8 Then run following command: java -jar ../picard.jar CreateSequenceDictionary REFERENCE=GRCh38.primary_assembly.genome.fa...

htsjdk.samtools.SAMException: Could not find dictionary next to reference file file:///data/sata_data/workshop/wsu29/Parivartan/snakemake_germline_legacy/references/GRCh38.primary_assembly.genome.fa

A Python library dedicated to NGS analysis (e.g., tools to visualise standard NGS formats). A set of pipelines dedicated to NGS in the form of Snakefiles (Makefile-like with Python syntax based on snakemake framework) with more than 80 re-usable...

Now a days there are a lots of genomics databases available around the world. This bookmark is created to provide all links in one place ... ftp://ftp.ncbi.nih.gov/genomes/ https://hgdownload.soe.ucsc.edu/downloads.html

This package consists of a series of functions created by the author (Jacob) to automate otherwise tedious research tasks. At this juncture, the unifying theme is the more efficient presentation of regression analyses. There are a number of...