clalign

Launch the workflow at the Latch console

CIAlign is a command line tool that allows users to remove specific issues from an MSA, visualise the MSA, and interpret the MSA.

Users can perfom the followig functions:

Cleaning an MSA

    - Remove insertions which are not present in the majority of sequences
    - Remove sequences below a threshold number of bases or amino acids
    - Crop poorly aligned sequence ends
    - Remove columns containing only gaps
    - Remove sequences above a threshold level percentage of divergence from the majority

Visualise alignments

    - Generate image files showing the alignment before and after analysis using 
    - showing which columns and rows have been removed
    - Draw sequence logos
    - Visualise coverage at each position in the alignment

Analyse alignment statistics

    - Generate a similarity matrix showing the percentage identity between each sequence pair 

Usage

For basic usage, user must input a fasta file with aligned sequence and a config file:

Downlaod the config file here

Edit the config file according to your needs.

The config file included in the description returns analysis with default values

Downlaod an example fasta file here for dummy use

Click Input File to enter the input file and Configs to enter the config file

Clck Launch Workflow button at LatchBio to begin the run

Accessing files

With a complete run, you can access the folowing files:

File with cleaned alignments

"Cleaned" alignment as cleaned.fasta

Consensus Sequence

consensus_sequence.fasta: containing consensus sequence only

cleanedWconsensus_sequence.fasta containing the cleaned alignment plus the consensus

Mini Alignments

view_input.jpg: with the the input alignment

view_output.jpg: with the the cleaned output alignment

view_markup.jpg: with the the input alignment with deleted rows and columns marked

Logos

logosBar.jpg: the alignment represented as a bar chart

logosTxt.jpg: the alignment represented as a standard sequence logo

Coverage Plots

CPlots_in.jpg : image showing the input alignment coverage

CPlots_out.jpg : image showing the output alignment coverage

Similarity Matrices

stats_in.tsv: similarity matrix for the input file

stats_out.tsv: similarity matrix for the output file

Head to Data on the latch console to access various files