Results for "MS"
Bio-Scripts
Perl script to find the distance beetween all the contigs and scaffolds
...$tmpFile > MAFFT_out"); #usage: perl clustalRead.pl MAFFT_out my ($seqRef, $ids) = fastafile2hash('MAFFT_out'); my ($fval, $sval) = trimMSA($seqRef->{$ids->[0]}{seq}, $...2155 days ago
Perl script to run SATSUMA in loop !
#!/usr/bin/perl -w use strict; use File::Temp qw(tempfile); # Usage perl 1by1.pl for SATSUMA analysis # User need to set the reference multifasta file name he...2155 days ago
Long reads mapper bash script !
.../bin/bwa ngmlrLoc=/home/urbe/Tools/ngmlr/bin/ngmlr-0.2.3/ngmlr lamsaLoc=/home/urbe/Tools/LAMSA/lamsa #Parameters accepte...$longReads -t $thread > $fileName.out.sam elif [ $toolName == "lamsa" ]; then echo "Mapping w...2138 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, '2140 days ago
- ...e download_reads: output: "rnaseq/raw_data/{sample}.fq.gz" params: # dynamically gener...rds: sample_links[wildcards.sample] shell: """ curl -L {params.download_link} -o {output}...
1531 days ago
- ...ng CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/SamSequence.cpp.o [ 27%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/SamSequenceDictionary.cpp.o [ 28%...
2114 days ago
Installing Busco version 4.0.6
...l-module-load-conditional-0.68-pl526_2 perl-module-metad~ bioconda/linux-64::perl-module-metadata-1.000036-pl526_0 perl-params-check bioconda/linux-64::perl-params-check-0.38-pl526_1 perl-pa...1468 days ago
- ...USAGE: [-h] Available Programs: ---------------------------...ToSam (Picard) Transforms raw Illumina sequencing data...mine if two potentially identical BAMs have the same duplicate reads...its a SAM or BAM file to multiple BAMs. UmiAwareMarkDuplicatesW...
2090 days ago
- ...2 +- lib/prompt_info_functions.zsh | 2 +- lib/spectrum.zsh | 2 +- lib/termsupport.zsh...
2090 days ago
Generate simulated polyploid genome !
#Generate 3% divergence msbar -point 4 -count 16558 toy.fasta > toyheterozygous3percent.fasta #Cat both files cat toy.fasta toymutated3percent.fasta > toyheterozygous3perce...2068 days ago
