github.com - pbalign aligns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5) format. The output Compare HDF5 file...
Meaningful analysis of next-generation sequencing (NGS) data, which are produced extensively by genetics and genomics studies, relies crucially on the accurate calling of SNPs and genotypes. Recently developed statistical methods both improve and...
Young computational biologist named Yaniv Erlich shocked the research world by showing it was possible to unmask the identities of people listed in anonymous genetic databases using only an Internet connection
github.com - snakePipes are flexible and powerful workflows built using snakemake that simplify the analysis of NGS data.
DNA-mapping*
ChIP-seq*
RNA-seq*
ATAC-seq*
scRNA-seq
Hi-C
Whole Genome Bisulfite Seq/WGBS
(*Also available in...
github.com - ClinCNV detects CNVs in germline and somatic context in NGS data (targeted and whole-genome). We work in cohorts, so it makes sense to try ClinCNV if you have more than 10 samples (recommended amount - 40 since we estimate variances from...
csb5.github.io - LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or...
github.com - Key features
Filters SNVs from any variant caller to remove false positives
Calculates metrics based on BAM files and provides filtering not possible with other tools
Fully user-configurable filtering (including which filters to use and their...
qualimap.bioinfo.cipf.es - Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like...