gabefoley/seqscrub

Website for cleaning FASTA headers and newick strings

SeqScrub

Website for cleaning FASTA headers and newick strings

SeqScrub is now live at www.gabefoley.com/seqscrub

Upload a FASTA file and optionally a tree file in Newick format, and SeqScrub can clean up, annotate and check for obsolete sequences all in the click of a button!

SeqScrub was published in BioTechniques in 2019.

doi.org/10.2144/btn-2018-0188

If you use it, please cite -

Foley G, Sützl L, D'Cunha SA, Gillam EM, Bodén M. SeqScrub: a web tool for automatic cleaning and annotation of FASTA file headers for bioinformatic applications. Biotechniques. 2019 Aug;67(2):50-54. doi: 10.2144/btn-2018-0188. Epub 2019 Jun 20. PMID: 31218882.

seqscrub's Issues

Remove carriage returns and white spaces from sequences

Include an option to remove carriage returns and white spaces from sequences

Allow large data set sizes

Currently we recommend to split data sets up if they get above 1000, but this should ideally be handled entirely within SeqScrub and we should allow data sets of any size.

Downloading 'bad character' output doesn't work when not mapping to databases

If you choose not to map to databases and search for bad characters, the bad character output is displayed in the output box (up to 100 sequences) but is not correctly included in the downloaded zip file.

Data does not refresh when additional data set is uploaded

If you upload a data set and annotate files, then upload another data set it adds these annotations to the first data set.

Add comment about checking upper and lower case 'bad characters'

In order to keep it flexible, we allow users to search for both upper and lower case (i.e. don't just convert the case) when searching for bad characters.

However, this should be made explicit by setting the default 'bad characters' as 'B J O U X Z b j o u x z' and adding a reference to it in the documentation.