| Pipelines |
CloudMap |
https://usegalaxy.org/cloudmap (Links to pipelines for the mapping methods are therein.) |
|
CloudMap PDF guide small |
https://usegalaxy.org/u/gm2123/d/3e04112cbed0be19 |
|
CloudMap video guide to Hawaiian variant mapping |
https://vimeo.com/51082571 |
|
MiModD |
http://mimodd.readthedocs.io/en/latest/index.html |
| Galaxy |
Galaxy main |
https://usegalaxy.org |
|
Galaxy wiki |
https://wiki.galaxyproject.org |
|
Learn Galaxy |
https://wiki.galaxyproject.org/Learn |
|
Public Galaxy servers |
https://wiki.galaxyproject.org/PublicGalaxyServers |
|
Using Galaxy in the Cloud |
https://wiki.galaxyproject.org/CloudMan |
|
Locally installing Galaxy |
https://wiki.galaxyproject.org/Admin/GetGalaxy |
|
Galaxy NGS 101 |
https://wiki.galaxyproject.org/Learn/GalaxyNGS101 |
|
Galaxy support |
https://wiki.galaxyproject.org/Support |
| File formats |
List of main filetypes |
https://en.wikipedia.org/wiki/Biological_data |
|
List of main filetypes |
http://www.genome.ucsc.edu/FAQ/FAQformat.html |
|
Phred quality scores |
https://en.wikipedia.org/wiki/Phred_quality_score |
| Main tools |
FastQC (quality control) |
http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
|
Sickle (FASTQ trimming) |
https://github.com/najoshi/sickle |
|
BWA (alignment) |
http://bio-bwa.sourceforge.net |
|
SAMtools |
http://www.htslib.org |
|
GATK suite (realign, variant calling) |
https://www.broadinstitute.org/gatk/ |
|
GATK best practices |
https://www.broadinstitute.org/gatk/guide/best-practices |
|
Picard (remove duplicates) |
http://broadinstitute.github.io/picard/ |
|
SnpEff and SnpSift (variant annotation/filtration) |
http://snpeff.sourceforge.net |
|
Bedtools (genome coverage) |
http://bedtools.readthedocs.io/en/latest/ |
