| 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. |
| Clustal Omega |
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 |
gfClient host port seqDir in.fa out.psl |
A client for the genomic finding program that produces a .psl file |
| 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. |
| soap |
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 |
soap -a <reads_a> -D <index.files> -o <output></output> |
For alignment of single-end reads |
| samtools fastq |
samtools fastq [options] in.bam |
Converts a BAM or CRAM into either FASTQ or FASTA format depending on the command invoked. |
| Cuffmerge |
cuffmerge [options]* <assembly_GTF_list.txt> |
cuffmerge can be used to merge together several Cufflinks assemblies. |
| tophat |
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. |