Mapping

hisat2
Function: Mapping RNA-seq reads with hisat2
Usage: hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <sam>]
Supported input format: FASTA, FASTQ
hisat2-build
Function: hisat2-build builds a HISAT2 index from a set of DNA sequences.
Usage: hisat2-build [options]* <reference_in> <ht2_base>
STAR
Function: Mapping RNA-seq reads with STAR
Usage: STAR --genomeDir /path/to/genomeDir --readFilesIn /path/to/read1 [/path/to/read2] --runThreadN NumberOfThreads --option1-name option1-value(s) ...
Supported input format: FASTQ
Bowtie2
Function: 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.
Usage: bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r> | --interleaved <i> | -b <bam>} [-S <sam>]
STAR
Function: Generating genome indexes for STAR
Usage: STAR --runMode genomeGenerate --option1-name option1-value(s) ...
Supported input format: FASTA
2bwt-builder
Function: Build index files for the reference genome before running SOAP
Usage: 2bwt-builder <FastaPath/YourFasta>
bwa
Function: 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).
Usage: 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]
bamCompare
Function: 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.
Usage: bamCompare -b1 treatment.bam -b2 control.bam -o log2ratio.bw
gfServer
Function: 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
Usage: gfServer status host port
makeblastdb
Function: Create Local BLAST Database
Usage: makeblastdb -in input_reads.fasta -dbtype [nucl|prot] -out input_reads_db
bwa
Function: 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.
Usage: 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>
blat
Function: Fast sequence search command line tool
Usage: blat database query [-ooc=11.ooc] output.psl
hisat2-inspect
Function: 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.
Usage: hisat2-inspect [options]* <ht2_base>
maq map
Function: Map reads to the reference sequences.
Usage: 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
bwa
Function: Generate alignments in the SAM format given paired-end reads. Repetitive read pairs will be placed randomly.
Usage: bwa sampe [-a maxInsSize] [-o maxOcc] [-n maxHitPaired] [-N maxHitDis] [-P] <in.db.fasta> <in1.sai> <in2.sai> <in1.fq> <in2.fq> > <out.sam>