Mapping

Function: For alignment of single-end reads

Usage: crac -i <index\_file> -k <int> -r <reads\_file1> -o <output\_file> --nb-threads <int>

Function: This tool takes an alignment file in SAM or BAM format and feature file in GFF format and calculates the number of reads mapping to each feature. It uses the htseq-count script that is part of the HTSeq python module

Usage: htseq-count [options] sam_file gff_file

Function: 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.

Usage: 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]

Function: 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.

Usage: bowtie-inspect [options]* <ebwt_base>

Function: A client for the genomic finding program that produces a .psl file

Usage: gfClient host port seqDir in.fa out.psl

Function: For alignment of paired-end reads

Usage: crac -i <index\_file> -k <int> -r <reads\_file1> <reads\_file2> -o <output\_file> --nb-threads <int>

Function: Index database sequences in the FASTA format.

Usage: bwa index [-p prefix] [-a algoType] <in.db.fasta>

Function: For alignment of single-end reads

Usage: soap -a <reads_a> -D <index.files> -o <output></output>

Function: For alignment of paired-end reads

Usage: soap -a <reads_a> -b <reads_b> -D <index.files> -o <PE_output> -2 <SE_output> -m <min_insert_size> -x <max_insert_size>

Function: Generate alignments in the SAM format given single-end reads. Repetitive hits will be randomly chosen.

Usage: bwa samse [-n maxOcc] <in.db.fasta> <in.sai> <in.fq> > <out.sam>

Function: cuffmerge can be used to merge together several Cufflinks assemblies.

Usage: cuffmerge [options]* <assembly_GTF_list.txt>

Function: Converts a BAM or CRAM into either FASTQ or FASTA format depending on the command invoked.

Usage: samtools fastq [options] in.bam

Function: TopHat is a program that aligns RNA-Seq reads to a genome in order to identify exon-exon splice junctions. It is built on the ultrafast short read mapping program Bowtie.

Usage: tophat [options]* <genome_index_base> <reads1_1[,...,readsN_1]> [reads1_2,...readsN_2]

Function: Create a salmon index

Usage: salmon index [options] -t transcript.fa -i index_name

Supported input format: FASTA