- 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
gauravsablok@genome panscape main ? ./target/debug/panscape -h
panscape: analyzing pangenomes from reads to stats
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
paf-annotate annotate your pangenome paf alignment using gtf
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