Bioinformatics Data Analysis Pipeline- General Tools

Bioinformatics Data Analysis Pipeline- General Tools

Bowtie2

Ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences,
Reference: PMID: 22388286
Contact: Qin Ma
LEfSe

Determines the features (organisms, clades, operational taxonomic units, genes or functions) most likely to explain differences between classes by coupling standard tests for statistical significance with additional tests encoding biological consistency and effect relevance.
Reference: PMID: 21702898
Contact: Qin Ma
FastQC

A quality control tool for high throughput sequence data.
Reference: PMID: 21702898
Contact: Qin Ma
Samtools

Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format.
Reference: PMID: 33590861
Contact: Qin Ma
HISAT2

HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome.
Reference: PMID: 25751142
Contact: Qin Ma
Bwa

Software package for mapping DNA sequences against a large reference genome.
Reference: PMID: 19451168
Contact: Qin Ma
Bedtools

Versatile command line toolkit to analyze genomic features.
Reference: PMID:20110278
Contact: Qin Ma
Featurecounts

An efficient general purpose program for assigning sequence reads to genomic features.
Reference: PMID: 24227677
Contact: Qin Ma
Cutadapt

Tool used for adapter trimming.
Reference: https://doi.org/10.14806/ej.17.1.200
Contact: Qin Ma
Integrative Genomics Viewer

Viewer for sequence alignment data.
Reference: PMID: 21221095
Contact: Qin Ma
Nf-Core

A community effort to collect a curated set of analysis pipelines built using Nextflow.
Reference: PMID: 32055031
Contact: Qin Ma