Results for "aligned"
Bio-Scripts
Mapping with BWA-mem or BWA-sampe in one go with python script !
...pping 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 mode. BESST pr...2140 days ago
- ...ters based on alignments Filters are active when alignment data are present --aligned Dump only aligned sequences --unaligned...
2142 days ago
Installing Porechop on Ubuntu !
...trimmed off (0 to 100) (default: 90.0) --check_reads CHECK_READS This many reads will be aligned to all possible...2122 days ago
- ...thSeqScoreSpark Step 3: Classifies pathogen-aligned reads and generates abundance...qToSam (Picard) Converts a FASTQ file to an unaligned BAM or SAM file FilterSa...
2091 days ago
Corona variant calling steps !
...ir -p results/sam results/bam results/bcf results/vcf bwa mem trimmed_fastq_small/$filename > results/sam/$basename.aligned.sam samtools view -S -b results/sam/$basename.aligned.sam > results/bam/$basename.a...1061 days ago
Python script to finds extact similar sequence between two multi fasta files !
...for line in result_handle: fields = line.strip().split('\t') qseq = fields[0] # Extract the aligned query sequence (qseq) #print("Aligned Query Sequence:", qseq)...19 days ago
