Results for "alignment"
Bio-Scripts
...X object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/BamAlignment.cpp.o [ 18%] Building CXX ob...^ [ 59%] Building CXX object src/CMakeFiles/sniffles.dir/Alignment.cpp.o [ 60%] Building CXX ob...2096 days ago
- ...Prints read alignments in samtools pileup format...(BETA Tool) Prints read alignments in samtools pileup format...M/BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for un...
2072 days ago
Samtools commands for bioinformatician !
...rence fasta, needed to left align and normalize bcftools norm -f ./input_data/ref.fasta \ vars.vcf \ -o vars_indels_realigned.vcf ### show alignment # first arg is sorted bam fi...1600 days ago
Bash script to alignment of short reads against reference genome !
...13.raw.sorted.bam SRR1770413.bam ##Breaking it down by line: #alignment with bwa: bwa mem -t $threads...reference file name (bwa finds the indexes using this) and the input alignment files. The first file should...1556 days ago
- (JitMetaENV) ➜ assembly conda install -c bioconda prokka Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen sol...
1212 days ago
Install and set up i-adhore for synteny and wgd analysis ! -- step by step --
...6%] Building CXX object src/alignment/CMakeFiles/alignment.dir/GGAl...rc/CMakeFiles/i-visualize.dir/AlignmentDrawer.cpp.o [ 36%] Building...rget bmp [ 16%] Built target alignment [ 59%] Built target i-visual...stset/datasetI/arath_2_3_beta/AlignmentMultiplicon2.svg -- Installin...1201 days ago
- ...Real] default = 10.0 -m alignment view options: 0 = pairwise,...fault = 0 -o Output File for Alignment [File Out] Optional def...-X X dropoff value for gapped alignment (in bits) [Integer] defa...e locally optimal Smith-Waterman alignments [T/F] default = F -Y...
947 days ago
Identify genome-wide synteny with LASTZ alignment
...lkstrough how to identifiy genome-wide synteny markers based on LASTZ alignment. Step1：Mask the repeat seq...-norna -gff -xmall -lib custom.TE.lib_for_FF.fa FFChr1.txt Step2: Alignment using LASTZ and Chain/Net...514 days ago
Perl script to parse blast results and plot basic stats !
...t Identity: ", $entry->{PERCENT_IDENTITY}, "\n"; print "Alignment Length: ", $entry->{ALIGNMENT_LENGTH}, "\n"; print "E-...Percent Identity: $avg_percent_identity\n"; print "Average Alignment Length: $avg_alignment_lengt...91 days ago
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