bioinformatics 49 biology 19 genomics 19 python 17 sequence 12 annotation 12 fasta 10 assembly 9 dna 8 analysis 8 sequencing 8 genetics 7 DNA 7 vcf 7 bacteria 6 gene 5 exome 5 microbiology 5 protein 5 synteny 4 RNA 4 CRISPR 4 genes 3 genomes 3 liftover 3 reference 3 scaffolding 3 phage 3 tnseq 3 high-throughput 3 bed 3 classification 3 biopython 3 virus 3 ucsc 3 pipeline 3 snps 3 ANI 3 SNP 3 ortholog 3 RNA-seq 2 prodigal 2 correction 2 SNPs 2 bioconda 2 ensembl 2 nanopore 2 annotations 2 deep-learning 2 python3 2 metagenomes 2 gtf 2 probe 2 research 2 clustering 2 data cleaning 2 machine learning 2 mash 2 population structure 2 bioinformatics-analysis 2 metagenomics 2 variants 2 genetic 2 cell 2 algorithm 2 chromatin 2 genome-browser 2 gff 2 genome-annotation 2 database 2 harvest 2 mutation 2 orf 2 transposon 2 long-reads 2 ncbi 2 tn-seq 2 average-nucleotide-identity 2 mutagenesis 2 essentiality 2 taxonomy 2 primer 2 metagenome 2 metagenome-assembly 2 contigs 2 cython 2 crispr 2 transcriptomics 2 disease 2 genome-assembly 2 alignment 2 blast 2 reader 2 variant 2 variation 2 transcriptome 2 codon 2 completeness 2 graph 2 ncbi-blast 2