Laura Luebbert
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lauraluebbert.com
Laura Luebbert
@lauraluebbert.com
390 followers 450 following 9 posts
Sabeti lab PostDoc @ Broad Institute of MIT an Harvard
genetics, compbio, & viruses
www.lauraluebbert.com
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lauraluebbert.com
Does it come with an API? We could use this under the hood of gget blast as well

pachterlab.github.io/gget/
Introduction - gget
gget enables efficient querying of genomic reference databases
pachterlab.github.io
March 12, 2025 at 2:03 PM
Reposted by Laura Luebbert
martinsteinegger.bsky.social
Our Big Fantastic Virus Database (BFVD) contains protein structure predictions of major viral clades, enhanced by petabase-scale homology search and it's explorable on the web. Led by @eunbelivable.bsky.social
🌐 bfvd.foldseek.com
📄 academic.oup.com/nar/article/...
BFVD—a large repository of predicted viral protein structures
Abstract. The AlphaFold Protein Structure Database (AFDB) is the largest repository of accurately predicted structures with taxonomic labels. Despite provi
academic.oup.com
March 8, 2025 at 3:28 PM
lauraluebbert.com
Thank you!
March 2, 2025 at 10:57 PM
Reposted by Laura Luebbert
maltekuehl.com
With pytximport and tools like fastp by Shifu Chen, kallisto by the @lpachter.bsky.social lab and gget by @lauraluebbert.com et al, running a bulk RNA-sequencing analysis is now a 10 line bash script. (7/12)
Code for RNAseq analysis: # get example data from the European Nucleotide Archive wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR105/088/SRR10574388/SRR10574388_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR105/088/SRR10574388/SRR10574388_2.fastq.gz # get the human genome reference files from Ensembl with gget gget ref -d -w cdna,gtf homo_sapiens # create a transcript-to-gene mapping with pytximport pytximport create-map -i ./Homo_sapiens.GRCh38.113.gtf.gz -o tx2gene.csv --target-field gene_name # preprocess your FASTQ files with fastp fastp -i SRR10574388_1.fastq.gz -I SRR10574388_2.fastq.gz -o SRR10574388_1.fastq.gz -O SRR10574388_1.fastq.gz # quantify the reads with kallisto kallisto index -i index.idx Homo_sapiens.GRCh38.cdna.all.fa.gz kallisto quant -i index.idx -o ./SRR10574388 --paired-end SRR10574388_1.fastq.gz SRR10574388_1.fastq.gz # correct for isoform-usage bias, summarize at the gene-level and save as AnnData (or .csv) pytximport -i ./SRR10574388/ -t kallisto -m tx2gene.csv -o ./counts.h5ad # run your downstream analysis python differential_gene_expression.py
November 29, 2024 at 5:24 PM