Bioinformatics Data Analysis Pipeline- General Tools
Bioinformatics Data Analysis Pipeline- General Tools
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Bowtie2
Ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences,
Reference: PMID: 22388286
Contact: Qin Ma
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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
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Samtools
Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format.
Reference: PMID: 33590861
Contact: Qin Ma
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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
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Bwa
Software package for mapping DNA sequences against a large reference genome.
Reference: PMID: 19451168
Contact: Qin Ma
- Bedtools
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Featurecounts
An efficient general purpose program for assigning sequence reads to genomic features.
Reference: PMID: 24227677
Contact: Qin Ma
- Cutadapt
- Integrative Genomics Viewer
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Nf-Core
A community effort to collect a curated set of analysis pipelines built using Nextflow.
Reference: PMID: 32055031
Contact: Qin Ma