Results for "samtools"
Bio-Scripts
BASH script for SelfBLAST a genome
#!/bin/bash #self BLAST a genome -- Expecting you have blast and samtools installed in your system #Autho...$2 for you from $FASTAFILE -- MAKE SURE U HAVE ADDED CORRECT NAME" samtools faidx MergedContigs.fasta...2635 days ago
Extract fasta sequence with Ids with Bash script
#!/bin/bash while IFS='' read -r line || [[ -n "$line" ]]; do echo "Text read from file: $line" samtools faidx ONT.fasta $line > $line.faa done < "$1"2337 days ago
- # get total number of bases covered at MIN_COVERAGE_DEPTH or higher samtools mpileup mapping_result_sorted.bam | awk -v X="${MIN_COVERAGE_DEPTH}" '$4>=X' | wc -l 32876 # get lengt...
2193 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 paired read...2107 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.bai2166 days ago
- .../trinity_out_dir/chrysalis/inchworm.K25.L25.DS.fa.min100 /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/trinity_out_dir/both.fa | samtools view -@ 40 -F4 -Sb - | samtools sort -m 3355443200 -@ 40 -no...
2110 days ago
Long reads mapper bash script !
...nd make it visualization ready !" #Location of the tools samtools=/home/urbe/anaconda3/bin/samtools graphMapLoc=/home/urbe/Tools...!" fi echo "Getting files ready for visualization !" $samtools view -Sb $fileName.out.sam |...2106 days ago
- ....1-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_wr...Prints read alignments in samtools pileup format PileupSpar...
2058 days ago
Installing pb-assembly on Linux !
...SAMtools/1.3.1-foss-2016a HDF5/1.8.16...enovo_asm) [jnarayan@hmem00 ~]$ conda install samtools Fetching package metadata .....19.1 py27_1 conda-forge samtools 1.9...2017 days ago
- ...3:36:41-- https://github.com/samtools/htslib/releases/download/1.9/...am_io.h htslib-1.9/cram/cram_samtools.c htslib-1.9/cram/cram_samto...Wall -O2 -I. -c -o cram/cram_samtools.o cram/cram_samtools.c gcc -...o cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cra...
2002 days ago
