Hercules: a profile HMM-based hybrid error correction algorithm for long reads
...osing whether to use second or third generation sequencing platforms can lead to...ors in these reads. Using datasets from two DNA-seq BAC clones (CH17-157L1 and CH...17-227A2), and human brain cerebellum polyA RNA-seq, we show that Hercules-correc...2082 days ago
P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads
...is a novel scaffolding tool using Pair-end RNA-seq to scaffold genome fragments....e program could utilize Illumina Paired-end RNA-sequencing reads from target spec...sp;PEP_scaffolder ) for scaffolding genome sequences. The most important fea...2065 days ago
Qualimap2: Evaluating next generation sequencing alignment data
...a command-line interface to facilitate the quality control of alignment sequencing data and its derivativ...ure counts. Supported types of experiments include: Whole-genome sequencing Whole-exome sequencin...2061 days ago
Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads
...ring and assembling short reads produced by RAD-seq. First, Rainbow clusters read...apse heterozygote while discriminate repetitive sequences. At last, Rainbow uses...sults. Based on simulation and a real guppy RAD-seq data, we show that Rainbow is...2023 days ago
GeneOverlap: An R package to test and visualize gene overlaps
.... Tri-methylation on lysine 4 of histone H3 (H3K4me3) is associated with gene activation and its genome-wide enrichment can be mapped by using ChIP-seq experiments. Because of its a...1953 days ago
kallisto: a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data
...transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput s...lignment. On benchmarks with standard RNA-Seq data, kallisto can...hter, Near-optimal probabilistic RNA-seq quantification, Nature Biotec...1943 days ago
1942 days ago
ChIPulate: A Python3 framework to simulate read counts in a ChIP-seq experiment
ChIP-seq simulation pipeline, ChIPulate, we assess the impact of various biological and experimental sources of variation on several outcomes of a ChIP-seq experiment, viz., the recover...1866 days ago
1781 days ago
Snakemake workflow: dna-seq-gatk-variant-calling
This Snakemake pipeline implements the GATK best-practices workflow for calling small genomic variants.1744 days ago