MISO An open-source LIMS for NGS sequencing centres

1. Logging in

You need to log in to MISO LIMS in order to make changes to any LIMS entities. Logging in lets MISO record any changes you make on entities you have access to.

If you are a new user and have not been given a username and password, you will first need to contact your MISO administrator to get a username and password.

Try to log in now:

1. Click on https://misodev.pmgenomics.ca.
2. Enter your username (e.g. jdoe) and password and click the Login button.

If all goes well, you should see the MISO Dashboard and see a message at the top right: "Logged in as: jdoe".

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2. Checking Index Distance

When you run multiple libraries in a sequencing lane or partition, known as multiplexing, indices are used to identify the individual libraries and demultiplex (separate) the data afterwards. If two or more libraries in the pool have identical or near-identical indices, demultiplexing may be more difficult or even impossible. The Index Distance tool can help you identify indices which may be inadvisable to multiplex together.

1. In the Tools menu on the left, click Index Distance. This will take you to the Index Distance Tool.

2. Copy and paste the following index sequences into the box on the left:

   AAAAAAAA
   AAAAACCC
   CCAAACCC
   AAAAAAAA
   

3. Click Calculate. The results pane will show you that there is a duplicate (AAAAAAAA), and that two of the sequences are a near match, only differing by 2 bases. (AAAAACCC and CCAAACCC).

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3. Checking Indices of Different Length

When indices are of different lengths, only the length of the shorter index should be considered. Click Clear to reset the form and enter the following index sequences.

AAAAAA
AAAAAACC
GGAAAATT
GGGAAA

Click Calculate and you'll see in the results that when comparing a 6-base index to an 8-base index, only the first 6 bases are compared. Because of this, 'AAAAAA' and 'AAAAAACC' are considered duplicates, and the other two sequences are considered near-matches with only a 1-base difference.

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4. Checking Dual-Index Sequences

With dual indices, it isn't a problem if multiple libraries have one of the same index sequences, as long as the other index is different. It is the combination of both indices that must be unique. You can compare dual-index sequences by entering both indices together as one. For example, take the following indices:

Click Clear to reset the form and enter the combined sequences into the Index Distance Tool:

AAAAAACCCCCC
AAAAAATTTTTT
GAAAAACCCCCC

Click Calculate. Notice that the first two sequences are not considered duplicates even though index 1 is the exact same. Only the first and third sequences are considered near matches.

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5. Selecting Indices from MISO

Rather than copying them from another source, or typing in the index sequences yourself, you can also choose indices from MISO to compare.

1. Click Clear to reset the form.
2. From the Indices list below the form, select any 5 indices.
3. Click Add from the toolbar. The sequences will appear in the Indices box of the tool above.
4. Click Calculate to check for duplicates or near matches.