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hisat2-build hisat2-build [options]* <reference_in> <ht2_base> hisat2-build builds a HISAT2 index from a set of DNA sequences. hisat2-build outputs a set of 6 files with suffixes .1.ht2, .2.ht2, .3.ht2, .4.ht2, .5.ht2, .6.ht2, .7.ht2, and .8.ht2. In the case of a large index these suffixes will have a ht2l termination. These files together constitute the index: they are all that is needed to align reads to that reference. The original sequence FASTA files are no longer used by HISAT2 once the index is built. Show
hisat2 hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>] Mapping RNA-seq reads with hisat2 Show
2bwt-builder 2bwt-builder <FastaPath/YourFasta> Build index files for the reference genome before running SOAP Show
bamCoverage bamCoverage -b reads.bam -o coverage.bw Given a BAM file, this tool generates a bigWig or bedGraph file of fragment or read coverages. The way the method works is by first calculating all the number of reads (either extended to match the fragment length or not) that overlap each bin in the genome. The resulting read counts can be normalized using either a given scaling factor, the RPKM formula or to get a 1x depth of coverage (RPGC). In the case of paired-end mapping, each read mate is treated independently to avoid a bias when a mixture of concordant and discordant pairs is present. This means that each end will be extended to match the fragment length. Show
gfServer gfServer status host port gfServer v 35x1 - Make a server to quickly find where DNA occurs in genome.To set up a server:gfServer start host port file(s)Where the files are .nib or .2bit format files specified relative to the current directory.To remove a server:gfServer stop host portTo query a server with DNA sequence:gfServer query host port probe.faTo query a server with protein sequence:gfServer protQuery host port probe.faTo query a server with translated dna sequence:gfServer transQuery host port probe.faTo query server with PCR primersgfServer pcr host port fPrimer rPrimer maxDistanceTo process one probe fa file against a .nib format genome (not starting server):gfServer direct probe.fa file(s).nibTo test pcr without starting server:gfServer pcrDirect fPrimer rPrimer file(s).nib Show
Bowtie2 bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r>} -S [<hit>] Bowtie2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters to relatively long (e.g. mammalian) genomes. Bowtie 2 supports gapped, local, and paired-end alignment modes. Show
STAR STAR --runMode genomeGenerate --option1-name option1-value(s) ... Generating genome indexes for STAR Show
bwa bwa mem [-aCHMpP] [-t nThreads] [-k minSeedLen] [-w bandWidth] [-d zDropoff] [-r seedSplitRatio] [-c maxOcc] [-A matchScore] [-B mmPenalty] [-O gapOpenPen] [-E gapExtPen] [-L clipPen] [-U unpairPen] [-R RGline] [-v verboseLevel] db.prefix reads.fq [mates.fq] Align 70bp-1Mbp query sequences with the BWA-MEM algorithm. Briefly, the algorithm works by seeding alignments with maximal exact matches (MEMs) and then extending seeds with the affine-gap Smith-Waterman algorithm (SW). Show
bwa bwa aln [-n maxDiff] [-o maxGapO] [-e maxGapE] [-d nDelTail] [-i nIndelEnd] [-k maxSeedDiff] [-l seedLen] [-t nThrds] [-cRN] [-M misMsc] [-O gapOsc] [-E gapEsc] [-q trimQual] <in.db.fasta> <in.query.fq> > <out.sai> Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence. Show
maq maq map [-n nmis] [-a maxins] [-c] [-1 len1] [-2 len2] [-d adap3] [-m mutrate] [-u unmapped] [-e maxerr] [-M c|g] [-N] [-H allhits] [-C maxhits] out.aln.map in.ref.bfa in.read1.bfq [in.read2.bfq] 2> out.map.log Map reads to the reference sequences. Show
bwa bwa bwasw [-a matchScore] [-b mmPen] [-q gapOpenPen] [-r gapExtPen] [-t nThreads] [-w bandWidth] [-T thres] [-s hspIntv] [-z zBest] [-N nHspRev] [-c thresCoef] <in.db.fasta> <in.fq> [mate.fq] Align query sequences in the in.fq file. When mate.fq is present, perform paired-end alignment. The paired-end mode only works for reads Illumina short-insert libraries. In the paired-end mode, BWA-SW may still output split alignments but they are all marked as not properly paired; the mate positions will not be written if the mate has multiple local hits. Show
crac crac -i <index\_file> -k <int> -r <reads\_file1> -o <output\_file> --nb-threads <int> For alignment of single-end reads Show
STAR STAR --genomeDir /path/to/genomeDir --readFilesIn /path/to/read1 [/path/to/read2] --runThreadN NumberOfThreads --option1-name option1-value(s) ... Mapping RNA-seq reads with STAR Show
hisat2-inspect hisat2-inspect [options]* <ht2_base> hisat2-inspect extracts information from a HISAT2 index about what kind of index it is and what reference sequences were used to build it. When run without any options, the tool will output a FASTA file containing the sequences of the original references (with all non-A/C/G/T characters converted to Ns). It can also be used to extract just the reference sequence names using the -n/--names option or a more verbose summary using the -s/--summary option. Show
bwa bwa samse [-n maxOcc] <in.db.fasta> <in.sai> <in.fq> > <out.sam> Generate alignments in the SAM format given single-end reads. Repetitive hits will be randomly chosen. Show
bwa bwa index [-p prefix] [-a algoType] <in.db.fasta> Index database sequences in the FASTA format. Show
bwa bwa sampe [-a maxInsSize] [-o maxOcc] [-n maxHitPaired] [-N maxHitDis] [-P] <in.db.fasta> <in1.sai> <in2.sai> <in1.fq> <in2.fq> > <out.sam> Generate alignments in the SAM format given paired-end reads. Repetitive read pairs will be placed randomly. Show
crac crac -i <index\_file> -k <int> -r <reads\_file1> <reads\_file2> -o <output\_file> --nb-threads <int> For alignment of paired-end reads Show
bowtie-inspect bowtie-inspect [options]* <ebwt_base> bowtie-inspect extracts information from a Bowtie index about what kind of index it is and what reference sequences were used to build it. When run without any options, the tool will output a FASTA file containing the sequences of the original references (with all non-A/C/G/T characters converted to Ns). It can also be used to extract just the reference sequence names using the -n/--names option or a more verbose summary using the -s/--summary option. Show
bamCompare bamCompare -b1 treatment.bam -b2 control.bam -o log2ratio.bw This tool can be used to generate a bigWig or bedGraph file based on two BAM files that are compared to each other while being simultaneously normalized for sequencing depth. Show