Single User License


Lucid alignment viewer is currently in alpha, you can evaluate the development release for free. However, a license should be purchased for continued use.


Licenses are for all stable future versions, and unlocks useful extra features like bookmarking. Once again, science saves the day.



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Phone:(415)692-1089

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Simple Best Practices

Alignments


Lucid assumes your files meet the SAM/BAM format specifications. All alignments should be in a .bam file with an index .bam.bai file in the same directory. Files can be local or remote, and made by any algorithm as long as the output adheres to these specifications.

Reference Genomes


References are displayed along the top of Lucid, and should be in FASTA format (.fa or .fasta). The fasta index file in .fasta.fai should be in the same local or remote directory as the reference file. Search/jump works best when one fasta contains the whole reference.



Troubleshooting Samples

Demo Alignment File


A .bam file made using best practices and hosted on our server, can be streamed or downloaded.

http://lucidalign.com/download/demo_align.bam

Human Reference Files


This is a great reference by the Broad Institute, often used for human analysis.

 ftp://ftp.broadinstitute.org/
 pub/seq/references/Homo_sapiens_assembly19.fasta

Ensembl Species


Try out the sequencing data from more species than you can shake a stick at.

 ftp://ftp.ensembl.org/pub/current_bamcov

Human NA12878 Files


These are GIAB standardized samples. This location has files from most platforms.

ftp://ftp.ncbi.nih.gov/giab/ftp/data/NA12878 



Say Hi

Phone:(415)692-1089