--filter_by_index1 specify a file contains a list of barcodes of index1 to be filtered out, one barcode per line (string [=]) --filter_by_index2 specify a file contains a list of barcodes of index2 to be filtered out, one barcode per line (string [=]) --filter_by_index_thres...
-s, –strict <switch> : filter low quality reads strictly (default: off) -z, –minSize <int> : small insert size (default: 18) -p, –polyA <float> : filter poly A, percent of A, 0 means do not filter, (default: 0.7) -Q, –qualSys <int> : quality system, 1:illumina, 2:...
fastq_quality_filter命令根据高质量碱基所占的百分比对序列进行过滤,-q参数指定碱基质量阈值,高于该阈值的碱基认为是高质量碱基,-p指定高质量碱基百分比的阈值,低于该阈值的序列会被过滤掉,基本用法如下 fastq_quality_filter -q 20 -p 90 -i input.fq -o ...
fastq_quality_filter:根据质量值筛选过滤,质量值低于cutoff的将被过滤掉 fastq_quality_trimmer:根据质量值截取序列,质量值低的3’ end部分将会被截短,如果截取之后剩余长度不足最小长度阈值,则这条read将会被过滤掉 fastx_reverse_complement:取反向互补序列 fastx_collapser:输出每条序列及其出现的频数(duplication le...
qiime quality-filter q-score \ --i-demux qiime_out_manifest.qza \ --o-filtered-sequences demux-joined-filtered.qza \ --o-filter-stats demux-joined-filter-stats.qza 输出对象: demux-joined-filter-stats.qza: 统计结果。 demux-joined-filtered.qza: 数据过滤后结果。
fastqc -f fasqc *.fq.gz #-f参数可以设置对fastq、bam、sam文件进行质控 ## 过滤短序列 Ion Torrent,pacbio,nanopore测序的fastq文件序列长度并不相同,通常需要过滤较短的序列。 seqkit seq -m 150 XX.fastq.gz | gzip - >XX_filter_150.fq.gz #过滤小于150bp序列,并压缩输出 ...
-e, --average_qual if one read's average quality score <avg_qual, then this read/pair is discarded. Default 0 means no requirement (int [=0])length filterLength filtering is enabled by default, but you can disable it by -L or --disable_length_filtering. The minimum length requirement...
--参数设置介绍: SOAPnuke -1path_to_Fastq1 -2path_to_Fastq2 -T4-n0.1-l5-q0.5-Q2-G -51-o outdir -C path_to_cleanFastq1 -D path_to_cleanFastq2 # 参数说明-T 线程 #Adapter related:-n, --nRate FLOAT N rate threshold [0.05]-l, --lowQual INT low quality threshold [5]-q, -...
filter a simple filter for pair end fastq sqeuence range print fastq records in a range search search reads/motifs from fastq file grep grep fastq sequence by read id or full name stats summary for fastq format file [aliases: stat]