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* [Tutorial (Ubuntu 16.04):](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/tutorial.md#tutorial-ubuntu-1604) | ||
* [Docker setup](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/tutorial.md#docker-setup) | ||
* [Download and install docker](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/tutorial.md#download-and-install-docker) | ||
* [Download images from docker hub](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/tutorial.md#download-images-from-docker-hub) | ||
* [Choose directories](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/tutorial.md#choose-directories) | ||
* [Run a container instance](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/tutorial.md#run-a-container-instance) | ||
* [Troubleshooting Docker](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/tutorial.md#troubleshooting-docker) | ||
* [Conflict with the container name](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/tutorial.md#conflict-with-the-container-name) | ||
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* [Pipeline setup](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/pipelinesetup.md#pipeline-setup) | ||
* [Download a BLAST database from NCBI](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/pipelinesetup.md#download-a-BLAST-database-from-ncbi) | ||
* [Create a species_list.txt file](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/pipelinesetup.md#create-a-species_listtxt-file) | ||
* [Abbreviations of genus names](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/pipelinesetup.md#abbreviations-of-genus-names) | ||
* [Primer3 settings](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/pipelinesetup.md#primer3-settings) | ||
* [Exclude geneidentifier from BLAST](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/pipelinesetup.md#exclude-geneidentifier-from-blast) | ||
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* [Primerdesign](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/primerdesign.md#primerdesign) | ||
* [First run](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/primerdesign.md#first-run) | ||
* [Directory tree](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/primerdesign.md#directory-tree) | ||
* [Using user provided genomes](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/primerdesign.md#using-user-provided-genomes) | ||
* [batchassist.py](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/primerdesign.md#batchassistpy) | ||
* [Additional info blastseqs option](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/primerdesign.md#additional-info-blastseqs-option) | ||
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* [Troubleshooting](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/troubleshooting.md#troubleshooting) | ||
* [Report bugs and problems](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/troubleshooting.md#report-bugs-and-problems) | ||
* [GUI trouble](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/troubleshooting.md#gui-trouble) | ||
* [Delete files created by the docker container from the host.](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/troubleshooting.md#delete-files-created-by-the-docker-container-from-the-host) | ||
* [Setting the timezone for the container](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/troubleshooting.md#setting-the-timezone-for-the-container) | ||
* [Troubleshooting pipeline runs](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/troubleshooting.md#troubleshooting-pipeline-runs) | ||
* [Primer quality control](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/troubleshooting.md#primer-quality-control) | ||
* ["fatal error while working on {genus_species} check logfile "](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/troubleshooting.md#fatal-error-while-working-on-genus_species-check-logfile-) | ||
* [Naming of user provided genome assemblies](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/troubleshooting.md#naming-of-user-provided-genome-assemblies) | ||
* [Errors during download of genome assemblies](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/troubleshooting.md#errors-during-download-of-genome-assemblies) | ||
* [Restart / continue stopped pipeline runs](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/troubleshooting.md#restart--continue-stopped-pipeline-runs) | ||
* [Error during quality control of genome assemblies](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/troubleshooting.md#error-during-quality-control-of-genome-assemblies) | ||
* [Only a few core genes are reported](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/troubleshooting.md#only-a-few-core-genes-are-reported) | ||
* [Thousands of primer are reported and primer QC takes forever](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/troubleshooting.md#thousands-of-primer-are-reported-and-primer-qc-takes-forever) | ||
* [Exclude gene identifier (GI) from BLAST results](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/troubleshooting.md#exclude-gene-identifier-gi-from-blast-results) | ||
* [Taxonomic vagueness](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/troubleshooting.md#taxonomic-vagueness) | ||
* [nt BLAST DB / nt BLAST DB version 5](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/troubleshooting.md#nt-blast-db---nt-blast-db-version-5) | ||
* [Problems with BLAST results](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/troubleshooting.md#problems-with-blast-results) | ||
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* [Custom DB tutorial](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/customdbtutorial.md#custom-db-tutorial) | ||
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* [Advanced command line usage](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/cmdlineonly.md#advanced-command-line-usage) | ||
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* [Troubleshooting Docker](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/dockertroubleshooting.md#troubleshooting-docker) | ||
* [Overview Docker commands](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/dockertroubleshooting.md#overview-docker-commands) | ||
* [Conflict with container name or port](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/dockertroubleshooting.md#conflict-with-container-name-or-port) | ||
* [Docker setup](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/dockertroubleshooting.md#docker-setup) | ||
* [Download and install docker](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/dockertroubleshooting.md#download-and-install-docker) | ||
* [Download images from docker hub](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/dockertroubleshooting.md#download-images-from-docker-hub) | ||
* [Choose directories](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/dockertroubleshooting.md#choose-directories) | ||
* [Run a container instance](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/dockertroubleshooting.md#run-a-container-instance) | ||
* [Test the container](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/dockertroubleshooting.md#test-the-container) | ||
* [Time settings](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/dockertroubleshooting.md#time-settings) | ||
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* [Configuration of Docker with DNS and proxy server](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/dockerproxy.md#configuration-of-docker-with-dns-and-proxy-server) | ||
* [DNS server (Docker daemon)](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/dockerproxy.md#dns-server-docker-daemon) | ||
* [Proxy server (Docker daemon)](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/dockerproxy.md#proxy-server-docker-daemon) | ||
* [DNS server (Docker container)](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/dockerproxy.md#dns-server-docker-container) | ||
* [Proxy server (Docker container)](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/dockerproxy.md#proxy-server-docker-container) | ||
* [TLS termination (Docker container)](https://github.com/biologger/speciesprimer/blob/speciesprimerv2.2/docs/dockerproxy.md#tls-termination-docker-container) |
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