Results for "PacBio read correction"
Bio-Scripts
Perl script to read multi fasta sequence one by one
#!/usr/bin/env perl use strict; use warnings; #USAGE #perl rohanRun.pl seq.fa my $outfile='tmp.fa'; my $fastaSeq_ref = readfasta ("$ARGV[0]"); my %fasta...print OUT "$key\n$fastaSeq{$key}\n"; } sub readfasta...2274 days ago
Mapping with BWA-mem or BWA-sampe in one go with python script !
BAM files and mapping BESST requires sorted and indexed BAM files as input. Any read aligner + samtools can be used to obtain such files. Read pairs needs to be aligned in pai...sahlin/BESST/blob/master/scripts/reads_to_ctg_map.py) for obtaining..._B.fq /path/to/contigs.fasta --threads N w...2177 days ago
Perl subroutine for reading multifasta file !
sub readfasta { (my $file)=@_; my %sequence; my $header; my $temp_seq; #suppose fasta files contains multiple sequences; open (IN, "2197 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...2193 days ago
Perl subroutine to read genome/reads fasta file !
sub readSeqFromFasta{ my $file = $_[0]; my (%map,$id,$seq); open(IN,$file) or die("Cannot open file for reading $f...2186 days ago
- ...hase 1: Clustering of RNA-Seq Reads --------------------- ----...building a k-mer catalog from reads) -- -----------------------....6.6/trinity_out_dir/insilico_read_normalization/AIG_AAAOSW_8_2_...rinity-v2.6.6/trinity_out_dir/read_partitions/Fb_0/CBin_2 Monda...rinity-v2.6.6/trinity_out_dir/read_parti...
2180 days ago
- ➜ bin git:(master) ✗ ./fastq-dump --help Usage: ./fastq-d...split into individual reads --split-spot...et, otherwise - to individual reads -M|--minReadLen...ce Filters for individual reads Applied only with --sp...iginal sequence name -I|--readids...
2179 days ago
Install Parrot Virtual Machine !
#Parrot is a virtual machine designed to efficiently compile and execute bytecode for dynamic languages...Is standard C Inf/NaN handling present..............yes. auto::thread - Does your system have threads........1590 days ago
Long reads mapper bash script !
#!/bin/bash #only for LONG READS mapping #USAGE: runMapper.sh minimap2 ref.fa reads.fa/fq 48 ont echo -e "This...$bwaMemLoc mem $refFasta $longReads -t $thread > $fileName.out.s...t.sam elif [ $readsType == "pacbio" ]; then $lamsaLoc aln -t $thread -T pacbio $refFasta $longReads > $fil...2175 days ago
- ➜ BorisTrinityAssembly /home/urbe/Tools/transrate-1.0.3-linux-x86_64/tr...ce based (if --assembly is given) 2. read mapping based (if --left and...arated --left= Left reads file(s) in FASTQ format, com...nds [ INFO] 2018-07-13 14:54:34 : No reads prov...
2176 days ago
