Results for "bowtie2"
Blogs
Illumina based assembly pipeline steps !
Illumina Merge re-sequenced FastQ files (cat) Read QC (FastQC) Adapter trimming (fastp) Removal of host reads (Kraken 2; optional) Variant calling Read alignmen...924 days ago
Bookmarks
- NGS data are just a bunch of sequences, you have no idea which region in the genome each sequences comes from, which gene it represents...To know that you have to align...
2607 days ago
PuffAligner: a fast, efficient and accurate aligner based on the Pufferfish index
...urate and versatile aligner built on top of the Pufferfish index. PuffAligner is able to produce highly sensitive alignments, similar to those of Bowtie2, but much more quickly. While...792 days ago
Files
Bioinformatics approach to Boar Taint
...eq2000 to >10X average coverage. Short reads generated from these samples mapped to Sus Scrofa version 10.2 reference assembly using Bowtie2. Alignment file then used for...3836 days ago
Top-level pages
Frequent Paired-end reads (PE 2x100) mapping command lines
bowtie2 -x hs37m -X 650 -q -1 r1.fq -2 r2.fq -S r12.bowtie2.sam bwa aln hs37m.fa r1.fq > r1.sai && bwa aln hs37m.fa r2.fq > r2.sai \ && bwa sampe hs37m r1.sai r...2229 days ago
Frequent parameters for bioinformatics tools !
...0 --min_mean_q 85 --min_window_q 65 FastQ Screen --aligner bowtie2' (bwa for PacBio) --subset 1...VF) -culling_limit 2 RGI (ABR) --input_type contig bowtie2 (mapping) --sensitive ...1332 days ago
Wire posts
Bio-Scripts
- ...higher samtools mpileup mapping_result_sorted.bam | awk -v X="${MIN_COVERAGE_DEPTH}" '$4>=X' | wc -l 32876 # get length of reference genome bowtie2-inspect -s refgenome | awk '{...
2256 days ago
- ...inchworm.K25.L25.DS.fa.min100 * Running CMD: /home/urbe/anaconda3/bin/bowtie2-build --threads 40 -o 3 /home...ull * Running CMD: bash -c " set -o pipefail;/home/urbe/anaconda3/bin/bowtie2 --local -k 2 --no-unal --thre...
2174 days ago
- +3 more Bio-Scripts
