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B
io
C
ode
a repository archiving codes for bioinformatics tools
WGS analysis
Base calling
Read quality control
Error correction
Duplicate read removal
Adapter trimming
WES analysis
Quality control
CNV detection
Somatic CNA detection
HLA typing
Allelic imbalance detection
De novo sequencing analysis
Genome assembly
Reference-assisted assembly
Assembly scaffolding
Assembly reconciliation
Assembly evaluation
RNA-seq analysis
Experimental design
Quality control
Spliced read alignment
De novo transcriptome assembly
Assembly evaluation
ChIP-seq analysis
Experimental design
Quality control
Peak calling
Peak annotation
Normalization
sRNA-seq analysis
tRNA-derived RNA annotation
miRNA mappers
ncRNA identification
IsomiR detection
ncRNA-related SNPs
BS-seq analysis
Experimental design
Quality control
Read alignment
Methylation scoring
Differentially methylated region detection
Metagenomic sequencing analysis
Sequence contamination detection
Ribosomal gene prediction
Protein database search
Quality control
Assembly
MeRIP-seq analysis
RNA-BSseq
16S rRNA-seq analysis
Experimental design
Probe design
Chimera detection
Denoising
Homology-based taxonomic classification
CLIP-seq analysis
RNA motifs discovery
miRNA target identification
Pipelines
Hi-C analysis
Read alignment
Quality control
Contact matrix generation
Contact matrix normalization
Peak calling
Amplicon sequencing analysis
GBS analysis
Pool-seq analysis
Demultiplexing
SNP detection
Indel detection
Transposon detection
Population genetic analysis
RAD-seq analysis
Rep-seq analysis
Strand-seq analysis
Deep mutational scanning analysis
GRO-seq analysis
Tn-seq analysis
CAGE analysis
scRNA-seq analysis
DGE analysis
dRNA-seq analysis
RNA structurome analysis
De novo ChIP-seq analysis
DNase-seq analysis
MNase-seq analysis
Nucleosome positionning analysis
Ribo-seq analysis
ChIP-exo analysis
HT-SELEX analysis
Degradome-seq analysis
MeDIP-seq analysis
MethylCap-seq analysis
oxBS/TAB/fCAB/CAB-seq
Metatranscriptomic sequencing analysis
CRISPR/Cas9 screen analysis
Drop-seq analysis
ChIA-PET analysis
3D structure prediction
ATAC-seq analysis
Nucleosome positionning analysis
scDNA-seq analysis
Single-cell assemblers
3C-seq analysis
4C-seq analysis
5C-seq analysis
3D structure prediction
RIP-seq analysis