2245 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...2117 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 >...2134 days ago
2116 days ago
2069 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...2059 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...2056 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...969 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...88 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...88 days ago