panscape

• from reads to alignments to pangenome, metagenome inclduing the genome annotation using the nanopore and pacbio under one rust binary
• this will also creates the pangenome database and also the pangenome reads database for rest api.
• added the support for the pangenome bed files and also the creation of the ancestral states from the bedfiles of the pangenomes.
• this code will be updated regularly.

cargo build

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panscape: analyzing pangenomes from reads to stats about
      ************************************************
      Gaurav Sablok,
      Email: codeprog@icloud.com
     ************************************************

Usage: panscape <COMMAND>

Commands:
 fasta-convert             convert into fasta
 clipper-align             clipping the regions from the fastq
 scanner                   scans the reads for the motifs single occurence
 motifcatcher              motif plus upstream and the downstream
 selectedreads             selected reads writer
 filterreads               filter the reads prior to the length
 clip-seq                  remove the clip regions from the reads
 multi-clip-seq            remove the multitags for the fastqfile
 pangenome                 assemble pangenome
 minimap                   annotate reads
 stat                      annotated stats for your file
 pangenome-summarize       pangenome pre-computed alignment
 read-multisearch          multisearch reads across the reads
 harmonicmean              estimate the harmonic mean from the pangenome
 pangenome-matcher         pangenome matcher
 pan-arc                   pangenome annotator
 snatcher                  extract specific region from paf alignment
 precomputed-paf           generate stats from precomputed paf
 precompute-cds            extract the coding regions from the precomputed pangenome
 graph                     graph analyzer
 pangenome-bed             Pangenome bed constructor
 intergenic-noncoding      Intergenic extractor
 pan-reads-database        pangenome database
 bedtool-ancestral         analyze pangenome from the bedtools alignment to ancestral state
 vcf-aanalyze              analyze pangenome vcffiles
 pangenome-single-merge    merge single pangenome bedfile
 multi-bedtools-ancestral  bedtools sncestral multi-pangenome
 help                      Print this message or the help of the given subcommand(s)

Options:
 -h, --help     Print help
 -V, --version  Print version

Gaurav Sablok
codeprog@icloud.com