Results for "SAM tool"
Bio-Scripts
Palindrome Simulation commands !
...lindromeSimulated.fa 3319 ~/Tools/art_bin_MountRainier/art_illumina -ss MSv3 -sam -i allPalindromeSimulated.fa...-s 10 -o paired_dat 3320 ~/Tools/art_bin_MountRainier/art_illumina -ss MSv3 -sam -i allPalindromeSimulated.fa -...PE.fasta 3326 cd masurca; ~/Tools/MaSuRCA-3.2.3/bin/masurca si...1724 days ago
Bash script to convert SAM to BAM visualization ready
samtools view -bS file.sam | samtools sort - file_sorted samtools index test_sorted.bam test_sorted.bai2171 days ago
- ...o to limit matepair distance on the same reference Filters for in...--legacy-report use legacy style 'Written spots' for tool ./fastq-dump : 2.9.1 ( 2....
2114 days ago
Long reads mapper bash script !
...ready !" #Location of the tools samtools=/home/urbe/anaconda3/bin/samtools graphMapLoc=/home/urbe/...resent at $refFasta" if [ $toolName == "bwa" ]; then echo...ds -t $thread > $fileName.out.sam elif [ $readsType == "pacbio...e: ont, pacbio" fi elif [ $toolName == "ngmlr" ]; then ec...2111 days ago
Installing Porechop on Ubuntu !
➜ Tools git:(master) ✗ git clone https://github.com/rrwick...869/869), done. Checking connectivity... done. ➜ Tools git:(master) ✗ cd Porechop...IN_SPLIT_READ_SIZE] [-h] [--version] Porechop: a tool for finding adapters in Oxfor...2094 days ago
- ...sv git:(master) pip install pysam Requirement already satisfied: pysam in /home/urbe/anaconda3/lib/p...MakeFiles/BamTools-static.dir/SamHeader.cpp.o [ 22%] Building C...%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/Bam.../BamTools-static.dir/internal/sam/SamFormatParser_p.cpp.o [ 53%...
2087 days ago
- ...[] Usage template for all tools (uses --spark-runner LOCAL when used with a Spark tool) gatk AnyTool toolArgs...cal.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async...that manipulate read data in SAM, BAM or CRAM format AddCo...
2063 days ago
- (denovo_asm) [jnarayan@hmem00 ~]$ git clone https://github.com/cdunn2001/git-sym.git fatal: destination path 'gi...0 0:03:26 0:00:02 0:03:24 94945greg200k-sv2.2/README.txt greg200k-sv2.2/SAM....
2022 days ago
- ➜ Tools git:(master) ✗ wget https://github.com/samtools/htslib/releases/download/1....3:36:41-- https://github.com/samtools/htslib/releases/download/1....am_io.h htslib-1.9/cram/cram_samtools.c htslib-1.9/cram/cram_samt...ex.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/...
2007 days ago
Installing Platypus on Ubuntu !
...gcc -g -Wall -O2 -I. -c -o sam.o sam.c gcc -g -Wall -O2 -I. -c -...n1 install -p -m 644 faidx.5 sam.5 vcf.5 /usr/local/share/man/m...ter release! File: /home/urbe/Tools/Platypus/src/cython/fastafil...-prototypes -fPIC -Itabix -Ipysam -I/home/urbe/anaconda3/envs/py...2007 days ago
