Results for "contigs"
Bio-Scripts
# generate dotplot lastdb test/ref.fa lastal -f TAB test/ref.fa test/contigs.reduced.pacbio.fa | last-dotplot - test/contigs.reduced.pacbio.fa.ref.png lastal -f TAB test/ref.fa test/contigs.reduced.nanopore.fa | last-dotplot - test/contigs.reduced.nanopore.fa.ref.png2257 days ago
Mapping with BWA-mem or BWA-sampe in one go with python script !
...BWA-sampe in one go. An example call for mapping with this script is python reads_to_ctg_map.py /path/to/lib1_A.fq /path/to/lib1_B.fq /path/to/contigs.fasta --threads N where N is...2129 days ago
Perl script to find the distance beetween all the contigs and scaffolds
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; $| = 1; #Script to see the distance beetween all the contigs and scaffolds #Usage: perl clustalReads.pl genome.fa >...2145 days ago
- ...er of threads to use (default: 8) --merge-assemblies= Merge best contigs from multiple assemblies into...g to /media/urbe/MyPassport/BorisTrinityAssembly/transrateSTAT/Trinity/contigs.csv [ INFO] 2018-07-13 14:54...
2128 days ago
- ...MSpark (EXPERIMENTAL Tool) Examines alignments of chimeric contigs, attempting to produce an opt...tsFromContigAlignmentsSAMSpark (BETA Tool) (Internal) Examines aligned contigs from local assemblies and cal...
2080 days ago
Perl script to extract a sequence from multifasta with range !
# filterfastarange.pl #!/usr/bin/perl use strict; use warnings; #perl filterfastarange.pl 301 600 contigs.fasta > contigs-gt300-lte600.fasta my $minlen = shift or die "Error: `minlen...2071 days ago
Perl script to break the contigs by 'N'
#!/usr/bin/perl -w use Bio::SeqIO; use strict; my $fasta = Bio::SeqIO->new( -file => "$ARGV[0].parts.fasta",-format=>'fasta'); open(SCAFF,">$ARGV[0].parts.scaff...2068 days ago
Tadpole is 250x faster than SPADes assembler !
...on: Uses kmer counts to assemble contigs, extend sequences, or error...fq,null mode=correct Extending contigs with reads could be done like...parameters: out= Write contigs (in contig mode) or corrected...tension=2 (mine) Do not keep contigs that did not extend at least...981 days ago
Perl script to calculate the basic stats of the assembled genome !
...ng statistics my $total_length = 0; my $num_contigs = 0; my @contig_lengths;...gth; $total_length += $length; $num_contigs++; push @contig_lengths,...l Length: $total_length\n"; print "Number of Contigs: $num_contigs\n"; print "Min...99 days ago
Python script for basic stats of the assembled genome !
...r computing statistics total_length = 0 num_contigs = 0 contig_lengths = [] #...ord.seq) total_length += length num_contigs += 1 contig_lengths.appe...l Length: {total_length}") print(f"Number of Contigs: {num_contigs}") print(f"Min...99 days ago
