Results for "Alignments !"
Bio-Scripts
BASH script for SelfBLAST a genome
...n echo "You want entire sequence to blast" SEQ=$FASTAFILE else echo "Something went wrong $USER - Contact jitendra" fi echo "Doing alignments -- BLASting"; blastn -task m...2662 days ago
- ...sequences starting or ending with >= 10N --qual-filter-1 Filter used in current 1000 Genomes data Filters based on alignments Filters are active whe...
2136 days ago
Installing Porechop on Ubuntu !
...be searched for adapter sequences (default: 150) --min_trim_size MIN_TRIM_SIZE Adapter alignments smaller than this will be ign...2116 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 unm...
2085 days ago
To convert just one specific read group to fastq
...bam/*.bam # Investigate the readgroups in the header. echo "" echo "SAM file header:" samtools view -H all.bam echo "" echo "Number of alignments with read group: GROUP-SRR197...1552 days ago
- ...nteger] default = 500 -b Number of database sequence to show alignments for (B) [Integer] defaul...teger] default = 0 -s Compute locally optimal Smith-Waterman alignments [T/F] default = F -Y...
960 days ago
BBmap the reads with all alignments !
bbmap.sh in=../reference/reference.numbered.fa ambig=all vslow perfectmode maxsites=100000 out=fetch_Ids_for_barcode.sam828 days ago
Script to rapid genome clustering based on pairwise ANI
...-db -outfmt '6 std qlen slen' -max_target_seqs 10000 -perc_identity 90 -o -num_threads 32 Next, calculate pairwise ANI by combining local alignments between sequence pairs: anica...645 days ago
