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bio-genome-assembly-hifi-assembly
hifiasm -o outputprefix -t 32 reads.hifi.fastq.gz awk '/^S/{print ">"$2;print $3}' outputprefix.bp.pctg.gfa > assembly.fasta hifiasm -o trioasm -t 32 ...
bio-genome-assembly-metagenome-assembly
Metagenome assembly reconstructs genomes from mixed microbial communities. Long reads enable recovery of complete circular genomes and resolution of s...
bio-genome-assembly-scaffolding
bwa index draftassembly.fa bwa mem -5SP -t 16 draftassembly.fa hicR1.fq.gz hicR2.fq.gz | \ samtools view -@ 8 -bhS - > aligned.bam pairtools parse --m...
bio-genome-engineering-off-target-prediction
Reference examples tested with: pandas 2.2+ Before using code patterns, verify installed versions match. If versions differ: Python: pip show <package...
bio-genome-intervals-gtf-gff-handling
GTF and GFF3 are standard gene annotation formats. Both use 1-based coordinates. | Feature | GTF | GFF3 | |---------|-----|------| | Coordinate system...
bio-genome-intervals-proximity-operations
Operations for finding nearby features and extending intervals using bedtools and pybedtools. bedtools closest -a peaks.bed -b genes.bed > peakswithne...
bio-hi-c-analysis-compartment-analysis
Reference examples tested with: cooler 0.9+, cooltools 0.6+, matplotlib 3.8+, numpy 1.26+, pandas 2.2+, scipy 1.12+ Before using code patterns, verify...
bio-hi-c-analysis-contact-pairs
Reference examples tested with: cooler 0.9+, pairtools 1.1+, pandas 2.2+ Before using code patterns, verify installed versions match. If versions diff...
bio-hi-c-analysis-hic-data-io
Reference examples tested with: cooler 0.9+, numpy 1.26+, pandas 2.2+, scanpy 1.10+, scipy 1.12+ Before using code patterns, verify installed versions...
bio-hi-c-analysis-hic-differential
Reference examples tested with: cooler 0.9+, cooltools 0.6+, matplotlib 3.8+, numpy 1.26+, pandas 2.2+, scipy 1.12+, statsmodels 0.14+ Before using co...
bio-hi-c-analysis-tad-detection
Reference examples tested with: cooler 0.9+, cooltools 0.6+, matplotlib 3.8+, numpy 1.26+, pandas 2.2+ Before using code patterns, verify installed ve...
bio-imaging-mass-cytometry-cell-segmentation
Reference examples tested with: Cellpose 3.0+, anndata 0.10+, matplotlib 3.8+, numpy 1.26+, pandas 2.2+, scanpy 1.10+, steinbock 0.16+ Before using co...