category: Sequence - DNA Sequencing and Assembly
programs:
ABySS - de novo sequence assembler
adaptercheck.py - Find potential read-through adapter contamination in sequencing reads
blreads - Process and analyze DNA sequencing reads
cutadapt - finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads
dipspades - assembler for highly polymorphic diploid genomes
fastq_pair - Remove non-paired reads from left or right read files
fixfq.py - Divide a fastq file into two files, one with validated reads, and the other with reads that do not comply with the fastq format
jellyfish - A fast k-mer counter
magicblast - search for reads which match a custom sequence database
pollux - DNA sequence read correction for all sequencing platforms
samtools - Utilities for the Sequence Alignment/Map (SAM) format
seqkit - FASTA/Q file manipulation
SOAPdenovo2 - denovo genome assembler
spades - Genome assembler
trim_galore - sequenc quality trimming and adaptor removal
Trimmomatic - Trim adaptors from sequencing reads
truspades - assembler for short reads produced by Illumina TruSeq Long Read technology