||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.
||clustalo -i input_file.fasta -o output_file.fasta [options]
||Clustal-Omega is a general purpose multiple sequence alignment (MSA) program for protein and DNA/RNA. It produces high quality MSAs and is capable of handling data-sets of hundreds of thousands of sequences in reasonable time.
||gfClient host port seqDir in.fa out.psl
||A client for the genomic finding program that produces a .psl file
||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.
||soap -a <reads_a> -b <reads_b> -D <index.files> -o <PE_output> -2 <SE_output> -m <min_insert_size> -x <max_insert_size>
||For alignment of paired-end reads
||soap -a <reads_a> -D <index.files> -o <output></output>
||For alignment of single-end reads
||samtools fastq [options] in.bam
||Converts a BAM or CRAM into either FASTQ or FASTA format depending on the command invoked.
||cuffmerge [options]* <assembly_GTF_list.txt>
||cuffmerge can be used to merge together several Cufflinks assemblies.
||tophat [options]* <genome_index_base> <reads1_1[,...,readsN_1]> [reads1_2,...readsN_2]
||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.