jasperboom / caltha Goto Github PK

Both the UMI SEQ and Centroid Read information can be found in the ZIP and BLAST file respectively.

VSEARCH produces centroid sequences for every input fasta file during the validation step of Caltha. These results might be useful for downstream analysis.

Caltha currently accepts only one fasta or fastq file as input. However, users need to process more than one fasta or fastq file at a time.

Parallel Processing in Python

Catlha currently exits with a error when the input is in fastq format.

Caltha currently requires users to input the format of the input file(s). Caltha should be able to automatically detect whether the input is in fasta or fastq format.

For every block in a UMI, count the occurrence of the 256 possible block variations. Output x number of block lists, one for every UMI block present.

Make sure to add a input for the user, number of blocks needs to be specified.

Rewrite the search algorithm to allow for one mismatch in the primer or adapter.

Possible libraries:

• BioPython
• Regex