references for pangenomes in the construction of expression compendia/pangenome mapping - Githubissues

greenelab / 2022-microberna

A pipeline to generate a compendia of bacterial and archaeal RNA-seq data

BSD 3-Clause "New" or "Revised" License

4 stars 1 forks source link

references for pangenomes in the construction of expression compendia/pangenome mapping #3

Open taylorreiter opened 2 years ago

taylorreiter commented 2 years ago

Application of a Novel “Pan-Genome”-Based Strategy for Assigning RNAseq Transcript Reads to Staphylococcus aureus Strains
- doi: 10.1371/journal.pone.0145861
PuffAligner: a fast, efficient and accurate aligner based on the Pufferfish index
- doi: 10.1093/bioinformatics/btab408
Ensembl Genomes 2022: an expanding genome resource for non-vertebrates
- doi: 10.1093/nar/gkab1007

taylorreiter commented 2 years ago

The quantitative impact of read mapping to non-native reference genomes in comparative RNA-Seq studies
- doi: 10.1371/journal.pone.0180904