Bowtie软件包的最初论文于2009年发表在《Genome Biology》上,题目是:“Ultrafast and memory-efficient alignment of short DNA sequences to the human genome”目前已被引用超20000余次 3用途简述 Bowtie2 是将测序reads与长参考序列比对的工具,适用于将长度大约为50到100或1000字符的reads与相对较长的基因组(如...
Remove internal iround loop and deal with it at the global loop instead Feb 9, 2024 aligner_sw.cpp Convert rfwbuf_ to fixed size Aug 1, 2024 aligner_sw.h Code cleanup: Use rdlen straight from swa Aug 27, 2024 aligner_sw_common.h ...
# 建索引 bwa index -a bwtsw ~/hg38.fa # 100bp长的双端测序reads的比对用bwa的mem算法 bwa mem -t 5 -R "@RG\tID:$sample\tSM:$sample\tLB:WGS\tPL:Illumina" /public/biosoft/GATK/resources/bundle/hg38/bwa_index/gatk_hg38 7E5241.L1_1.fastq 7E5241.L1_2.fastq | samtools sort -@...
I'm not actually getting an error message, but I think its stopping before it actually finishing the index (see below for the output). This is on version 2.3.4.1, I used bioconda to install. INFO: Command: bowtie2-build-s --wrapper basic-0 -f Humann2Test/A1HF_humann2_temp/A1HF_...
It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory...