Results for "Contig"
Bio-Scripts
Perl script to insert sequence in contig !!
# sub signature: #insertSEQintoCONTIGatLOC( SEQ , CONTIG , LOC ) ; sub insertSEQintoCONTIGatLOC{ my ( $SEQ , $CONTIG , $LOC ) = @_; substr( $CON...print 'insert = '.($s = insertSEQintoCONTIGatLOC( "CCCC ", $s , 26 ))."\n...2693 days ago
- bio
2453 days ago
Create genome scaffolding with Perl
...lt options my @pslFiles = (); my $projOpts = { "query" => 0, # contig file for query sequences "prefix" => "psl_scaffold_", # prefix for contig names "pid" => 90, # perc...2293 days ago
- ...----------- --------------- Inchworm --------------------- -- (Linear contig construction from k-mers) --...-------- -------------------- Chrysalis ------------------------- -- (Contig Clustering & de Bruijn Graph...
2111 days ago
- ...fault: 8) --merge-assemblies= Merge best contigs from multiple assemblies int...ity [ INFO] 2018-07-13 14:54:21 : Calculating contig metrics... [ INFO] 2018-07-1...0.0 [ INFO] 2018-07-13 14:54:34 : Contig metrics done in 13 seconds [...
2107 days ago
- ...s to produce denoised copy ratios DetermineGermlineContigPloidy (BETA Tool) Determines the baseline contig ploidy for germline samples g...(EXPERIMENTAL Tool) Examines alignments of chimeric contigs, attempting to produce an op...
2059 days ago
Perl script to break the contigs by 'N'
...my $seqobj = $fasta->next_seq() ) { #gets contig id my $contig = $seqobj->display_id(); #g...ks) #Hash nregions stores a hash from the contig id to the NNNNN regions found...$i=0;$itrunc($cini,$cend); my $new_id=$contig . "_p$cont"; $cont++;...2047 days ago
CollectGcBiasMetrics.jar will generate a GC bias plot for each contig
samtools index aln-pe.mapped.sorted.bam for i in $(samtools view -H aln-pe.mapped.sorted.bam | awk -F"\t" '/@SQ/{gsub("^SN:","",$2);print $2}' ); do samtools view -...1988 days ago
Tadpole is 250x faster than SPADes assembler !
...on: Uses kmer counts to assemble contigs, extend sequences, or erro...fq,null mode=correct Extending contigs with reads could be done lik...parameters: out= Write contigs (in contig mode) or correcte...Minimum kmer count to seed a new contig or begin extension. mincount...960 days ago
Perl script to calculate the basic stats of the assembled genome !
...statistics my $total_length = 0; my $num_contigs = 0; my @contig_lengths; # Iterate through...tional statistics my $min_contig_length = $contig_lengths[-1]; my $max_contig_...int "GC Content: $gc_content%\n"; print "\nContig Length Distribution:\n"; pri...78 days ago
