Bioinformatics tools

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Description

This page lists the softwares cited in this wiki.

Authors

Authors	Christine Tranchant-Dubreuil
Research Unit	UMR DIADE
Institut

Date

10/03/2017

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Summary

• NGS preprocessing
• Mapping
• sam, bam files manipulating
• Variant calling
• Vcf manipulating`
• Viewer

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NGS preprocessing

| fastqc | a quality control tool for high-throughput sequence data (Babraham Institute) and is developed in Java. | | :------------- | :------------- | | cutadapt | removes adapter sequences from next-generation sequencing data |

Mapping

| bwa | bwa index
bwa aln, bwa sampe bwa samse
bwa mem | a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. | | :------------- | :------------- | :------------- |

Sam, bam files manipulating

| gatk | RealignerTargetCreator
IndelRealigner | Genome Analysis Toolkit - A package to analyse next-generation re-sequencing data, primary focused on variant discovery and genotyping.|
| :------------- | :------------- | :------------- | | picardtools | createDictionary
MarkDuplicates
sortSam| comprises Java-based command-line utilities that manipulate SAM files, and a Java API (SAM-JDK) for creating new programs that read and write SAM files. | | samtools | samtools inde_
samtools view<br > samtools flagstat, samtools idxstats | provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

Variant calling

| gatk | unifiedGenotyper
haplotypeCaller | Genome Analysis Toolkit - A package to analyse next-generation re-sequencing data, primary focused on variant discovery and genotyping. | | :------------- | :------------- | :------------- |

Vcf manipulating

| gatk | SelectVariants
VariantFiltration | Genome Analysis Toolkit - A package to analyse next-generation re-sequencing data, primary focused on variant discovery and genotyping. | | :------------- | :------------- | :------------- | | vcftools | | vcftools is a suite of functions for use on genetic variation data in the form of VCF and BCF files. The tools provided will be used mainly to summarize data, run calculations on data, filter out data, and convert data into other useful file formats. |

Viewer

| igv | bam, vcf | The Integrative Genomics Viewer (IGV) from the Broad Center allows you to view several types of data files involved in any NGS analysis that employs a reference genome, including how reads from a dataset are mapped, gene annotations, and predicted genetic variants. | | :------------- | :------------- | :------------- | | tablet | bam, vcf | Tablet is a lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments. |