Results for "alignment"
Bio-Scripts
Download genome using NCBI esearch command line !
...uery "NC_005956.1" | efetch -format fasta > seq1.fa esearch -db nucleotide -query "CP003784.1" | efetch -format fasta > seq2.fa #fastANI for alignment free comparision #conda inst...1085 days ago
Blast result parser with Perl and Bioperl
...# get the start and the end of the query sequence in the alignment print OUT $hsp->start('q...# get the start and the end of the hit sequence in the alignment print OUT $hsp->start('h...2898 days ago
Needleman-Wunsch Algorithm in Perl
....pl HEAGAWGHEE PAWHEAE BLOSUM50.txt -8 # See: "Biological sequence anaysis" Durbin et al. ed. CUP 1998, Pg. 19 # Needleman-Wunsch global alignment algo (GOTHO 1982 mod) # us...2889 days ago
Calculate some statistics for a DNA alignment with Perl
use Bio::AlignIO; use Bio::Align::DNAStatistics; my $stats = Bio::Align::DNAStatistics->new(); my $alignin = Bio::AlignIO->new(-format => 'emboss',...2633 days ago
Mapping with BWA-mem or BWA-sampe in one go with python script !
...e N is an integer specifying how many threads BWA-mem should use. --nomem can be specified to the above call to use BWA-sampe as the paired read alignment pipeline. https://github.c...2108 days ago
Biological Sequence handling with Perl !
...ence::Generic; use Sequence::Nucleotide::Subsequence; use Sequence::Alignment; use Carp; use strict; u...shift; $seq = $seq->seq if ref($seq); return new Sequence::Alignment(src=>$seq,target=>$self->seq)...2165 days ago
Perl script to run SATSUMA in loop !
#!/usr/bin/perl -w use strict; use File::Temp qw(tempfile); # Usage perl 1by1.pl for SATSUMA analysis # User need to set the reference multifasta file name here...2124 days ago
- ...ng or ending with >= 10N --qual-filter-1 Filter used in current 1000 Genomes data Filters based on alignments Filters are active when alignment...
2110 days ago
Perl script to merge LastZ overlaps
#!/usr/bin/perl use strict; use warnings; use 5.010; # Filter out the exact/direct overlaps from tab seperated alignment file. (lastz format=general- ready) # Do not inclide header in lastz outfile # USAGE: perl filterOverlaps.pl infile > outfile open my $fh, '2109 days ago
Installing Porechop on Ubuntu !
...src/adapter_align.o porechop/src/alignment.o Compiling Porechop: make -...-mtune=native -c -o porechop/src/alignment.o porechop/src/alignment.cpp...er of threads to use for adapter alignment (d...Adapter alignments smaller than this will be ig...2090 days ago
