User talk:Darek Kedra/sandbox 29: Difference between revisions
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== 00 Programs used == | == 00 Programs used == | ||
===sequence pre-processing== | |||
* [http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ FastQC] ver 0.11.2 | |||
* [http://www.usadellab.org/cms/index.php?page=trimmomatic Trimmomatic ] ver 0.32 | * [http://www.usadellab.org/cms/index.php?page=trimmomatic Trimmomatic ] ver 0.32 | ||
* [http://sourceforge.net/projects/tagdust/ TagDust] ver 2.13 | |||
=== general tools == | |||
* [http://hannonlab.cshl.edu/fastx_toolkit/ fastx_toolkit] ver 0.0.13 | |||
* [http://samtools.sourceforge.net/ Samtools classic] ver 0.1.19 | * [http://samtools.sourceforge.net/ Samtools classic] ver 0.1.19 | ||
* [http://www.htslib.org/ samtools/HTSlib] ver 1.0 | * [http://www.htslib.org/ samtools/HTSlib] ver 1.0 | ||
* [http://picard.sourceforge.net/ Picard ] ver 1.119 | * [http://picard.sourceforge.net/ Picard ] ver 1.119 | ||
=== mappers === | |||
* [http://bio-bwa.sourceforge.net/ BWA] ver 0.7.10 | |||
* [http://last.cbrc.jp/ LAST] ver 475 | |||
* [http://www.well.ox.ac.uk/~gerton/software/Stampy/ Stampy] stampy-1.0.23r2059.tgz (optional) | |||
==NGS file formats== | ==NGS file formats== | ||
Revision as of 08:11, 9 September 2014
EMBO Tunis 2014
From sequencing data to knowledge
00 Programs used
=sequence pre-processing
- FastQC ver 0.11.2
- Trimmomatic ver 0.32
- TagDust ver 2.13
= general tools
- fastx_toolkit ver 0.0.13
- Samtools classic ver 0.1.19
- samtools/HTSlib ver 1.0
- Picard ver 1.119
mappers
NGS file formats
- FASTQ
- SAM
- BAM,
- VCF,
- GTF/GFF
- BED
pre-processing FASTQ files =
Mapping Illumina reads with LAST (possibly also with BWA/Stampy: check with G.Benson) Quick and dirty genome 2 genome comparison using LAST Viewing mapping results with IGV SNP discovery Quantifications of mapped reads Finding gene ends by mapping post-splice leader and polyA sequences Mapping Illumina reads using LAST Comparing 2-3 Leishmania genomes Viewing mappings and SNPs Gene quantifications (DNA & RNA levels)
