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Aligns RNA-seq reads to a reference genome using uncompressed suffix arrays. STAR has a potential for accurately aligning long (several kilobases) reads that are emerging from the third-generation sequencing technologies.

A suite of programs for interacting with high-throughput sequencing data. \n It consists of three separate repositories:\n Samtools (Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format),\n BCFtools (Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants)\n and HTSlib (A C library for reading/writing high-throughput sequencing data). 'D

echo - display a line of text

pattern scanning and processing language

Write sorted concatenation of all FILE(s) to standard output. With no FILE, or when FILE is -, read standard input.

A suite of programs for interacting with high-throughput sequencing data. \n It consists of three separate repositories:\n Samtools (Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format),\n BCFtools (Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants)\n and HTSlib (A C library for reading/writing high-throughput sequencing data). sa

cat - concatenate files and print on the standard output

UCSC genome browser 'kent' bioinformatic utilities These are only the command line bioinformatic utilities from the kent source tree. Original tool usage: bedGraphToBigWig in.bedGraph chrom.sizes out.bw where in.bedGraph is a four column file in the format: <chrom> <start> <end> <value> and chrom.sizes is a two-column file/URL: <chromosome name> <size in bases> and

"Python scripts for running ENCODE atac-seq pipeline." ENCODE DCC generate HTML report and QC JSON.

"Python scripts for running ENCODE atac-seq pipeline." ENCODE DCC cross-correlation analysis.

"Python scripts for running ENCODE atac-seq pipeline." ENCODE DCC pseudo replicator.

"Python scripts for running ENCODE atac-seq pipeline." ENCODE DCC IDR. NarrowPeak or RegionPeak only.

"Python is a programming language that lets you work quickly and integrate systems more effectively."

"Python scripts for running ENCODE chip-seq-pipeline2" ENCODE DCC spp callpeak

"Python scripts for running ENCODE chip-seq-pipeline2" ENCODE DCC bwa aligner.

"Python scripts for running ENCODE chip-seq-pipeline2" ENCODE DCC Choose control. Choose appropriate control for each IP replicate. idx.txt will be generated on --out-dir. idx.txt contains zero-based index of control in each line for each IP replicate. -1 means pooled TAG-ALIGN.

Translate, squeeze, and/or delete characters from standard input, writing to standard output. Translate, squeeze, and/or delete characters from standard input, writing to standard output.