Shan Zhang¹ and Weizhi Song²

¹ Department of Pharmacology and Pharmacy, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong

² Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong

• BioSAK has been tested on Linux/Mac, but NOT yet on Windows.

• BioSAK is implemented in python3, you can

  • install it with pip3 install BioSAK

  • upgrade it with pip3 install --upgrade BioSAK

• If you are an UNSW Katana user, this might be helpful.

• You can get example commands for most of the modules by typing, for example, BioSAK iTOL -h.

• Please refer to the documentation page for help (in preparation, very messy).

• A license statement is here.

• A changelog is here.

• Type BioSAK -h to see a full list of modules

            ...::: BioSAK v1.121.0 :::...
  
  Genome databases
     get_GTDB_taxon_gnm      ->  Get id of genomes from specified GTDB taxons
     get_genome_GTDB         ->  Batch download GTDB genomes
     get_genome_NCBI         ->  Batch download GenBank genomes
     sampling_GTDB_gnms      ->  Select GTDB genomes
     subset_GTDB_meta        ->  Subset metadata of GTDB reference genomes
     metaAssembly            ->  Get metadata of NCBI assembly records
     metaBiosample           ->  Get metadata of NCBI biosample records
     statsTaxa               ->  stats GTDB taxa
     GenBank                 ->  get sequence/organism/voucher info
  
  Metagenomics
     metabat2concoct         ->  convert MetaBAT depth to CONCOCT depth
     metabat2maxbin          ->  convert MetaBAT depth to MaxBin depth
     CheckM                  ->  Parse CheckM outputs
     Plot_MAG                ->  plot MAGs, (GC vs depth)
     magabund                ->  Calculate MAG abundance
     mean_MAG_cov            ->  Get mean MAG depth (by MetaBAT depth)
     RunGraphMB              ->  Prepare input files for GraphMB
     gc                      ->  Get GC content
     get_gnm_size            ->  Get the total length of genome(s)
     get_gene_depth          ->  Get gene depth by contig depth
     MeanMappingDepth        ->  Get mean mapping depth 
     get_MAG_reads_long      ->  Extract MAG-specific long reads for reassembling
     mmseqs                  ->  Classify metagenomic contigs with mmseqs
     parse_mmseqs_tsv        ->  Parse mmseqs tsv
     fastaai                 ->  A wrapper for FastAAI
     abd                     ->  get MAG abundance across metagenomes (Wenxiu Wang et al. 2024)
     abd_mask                ->  prepare masked sequence for abd module
     
  Functional annotation
     KEGG                    ->  KEGG annotation
     koala                   ->  Separate the combined BlastKOALA or GhostKOALA output
     COG2020                 ->  COG annotation (v2020, by blastp/diamond)
     COG2024                 ->  COG annotation (v2024, by blastp/diamond)
     arCOG                   ->  COG annotation for archaea (version ar18)
     dbCAN                   ->  CAZy annotation with dbCAN
     Combine_KEGG_arCOG      ->  Combine KEGG and arCOG annotation results
     Combine_KEGG_COG        ->  Combine KEGG and COG annotation results
     enrich                  ->  Functional enrichment analysis
     gapseq                  ->  Data matrix GapSeq predicted pathways
     stats_ko                ->  get stats for a list of provided KO
     stats_arcog             ->  get stats for a list of provided arCOG 
     stats_cog2024           ->  get stats for a list of provided COG (v2024)
     combine_fun_stats       ->  combine outputs from stats_ko, stats_arcog or stats_cog2024
      
  16S rRNA related
     Usearch16S              ->  Usearch for Novogene 16S amplicon sequencing results
     blca                    ->  Classify 16S with BLCA
     top_16S_hits            ->  Classify 16S by top-blast-hits approach
     SILVA_for_BLCA          ->  Prepare BLCA-compatible SILVA SSU database
     GTDB_for_BLCA           ->  Prepare BLCA-compatible GTDB SSU database
     UNITE_for_BLCA          ->  Prepare BLCA-compatible UNITE SSU database
     BLCA_op_parser          ->  Make the BLCA outputs bit easier to read
     Tax4Fun2IndOTU          ->  Get functional profile for individual OTUs (to be added)
     get_eu_otu              ->  Get eukaryotic OTUs
     rm_low_abd_otu          ->  Remove low abd otu from table
     combine_low_abd_otu     ->  Combine low abundance OTUs
     rm_low_depth_sample     ->  Remove samples from OTU table with small number of sequences
  
  Sequence manipulator
     gbk2fna/gbk2faa/gbk2ffn ->  Format convertors
     ffn2faa/gfa2fa/get_rc   ->  Format convertors
     fq2fa                   ->  Convert fastq to fasta
     fa2id                   ->  Export sequence id
     slice_seq               ->  Get specified region of a sequence
     rename_seq              ->  Rename sequences in a file
     prefix_seq_by_file_name ->  prefix sequences by file name
     select_seq              ->  Select sequences by id
     split_fasta             ->  Split one fasta file into multiple files
     merge_seq               ->  Merge sequence files, remove duplicated ones if any
     cat_fa                  ->  Combine fasta files, prefix sequence id with file name
         
  Sam and Bam
     reads2bam               ->  Mapping and sorting
     sam2bam                 ->  Sam to BAM with samtools
     split_sam               ->  Split SAM/BAM file by reference
     bam2reads               ->  Extract reads (id) from sam file
     plot_sam_depth          ->  Plot SAM depth
  
  Dataframe and Statistics
     subset_df               ->  Subset dataframe
     merge_df                ->  Merge dataframes
     add_desc                ->  Add function description to input of the iTOL module
     transpose               ->  Transpose dataframe
     wilcox                  ->  Wilcoxon signed-rank test (non-parametric paired T-test)
     mannwhitneyu            ->  Mann-Whitney U rank test on two independent samples
  
  Others
     js_cmds                 ->  Put commands in job scripts
     js_hpc3                 ->  Put commands in job scripts (HKUST hpc3)
     hpc3                    ->  Submit jobs on HKUST hpc3
     srun                    ->  srun one-line commands on HKUST hpc3
     exe_cmds                ->  Execute commands with multiprocessing
     split_folder            ->  Split folder
     prefix_file             ->  Prefix file
     BestHit                 ->  Keep best blast hits (outfmt 6)
     VisGeneFlk              ->  Visualize gene flanking regions
     usearch_uc              ->  Parse Usearch uc file
     get_Pfam_hmms           ->  Get Pfam profiles by id
     Reads_simulator         ->  Simulate NGS reads
     SubsampleLongReads      ->  Subsample Long Reads
     rename_reads_Reago      ->  Rename paired reads for Reago
     cross_link_seqs         ->  Cross link matched regions between two sequences
     submitHPC               ->  A wrapper for submitHPC.sh
     KeepRemovingTmp         ->  Keep removing old files in a folder
     ribbon                  ->  Make a ribbon diagram
     compare_sets            ->  compare_sets
     sankey                  ->  get sankey plot
     sra                     ->  Download reads with sratoolkit
     vis_color_scheme        ->  Visualize color scheme
     trim                    ->  a wrapper for trimmomatic
     FasterqDump             ->  a wrapper for fasterq-dump
     rename_df_row           ->  rename row headers in a dataframe
     blast                   ->  Parse batch online blast output
     taxdump                 ->  Parse NCBI Taxonomy database
     get_single_page_web     ->  Get single page website